diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b290e09..237c9ed 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,20 +1,21 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh new file mode 100755 index 0000000..9f7188f --- /dev/null +++ b/.devcontainer/setup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +# Customise the terminal command prompt +echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc +echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc +export PROMPT_DIRTRIM=2 +export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' + +# Update Nextflow +nextflow self-update + +# Update welcome message +echo "Welcome to the nf-core/isoseq devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 72dda28..0000000 --- a/.editorconfig +++ /dev/null @@ -1,33 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore python and markdown -[*.{py,md}] -indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index db37ff5..0000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,125 +0,0 @@ -# nf-core/isoseq: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/isoseq. - -We try to manage the required tasks for nf-core/isoseq using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/isoseq then the best place to ask is on the nf-core Slack [#isoseq](https://nfcore.slack.com/channels/isoseq) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/isoseq, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/isoseq issues](https://github.com/nf-core/isoseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/isoseq repository](https://github.com/nf-core/isoseq) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. - -## Getting help - -For further information/help, please consult the [nf-core/isoseq documentation](https://nf-co.re/isoseq/usage) and don't hesitate to get in touch on the nf-core Slack [#isoseq](https://nfcore.slack.com/channels/isoseq) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the nf-core/isoseq code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test command in `.github/workflow/ci.yml`. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. - -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/isoseq/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b6eb7ba..8add760 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [nf-core/isoseq pipeline documentation](https://nf-co.re/isoseq/usage) - - type: textarea id: description attributes: diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 2d1bd6d..506aa25 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,16 +8,16 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/isoseq/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/isoseq/tree/master/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/isoseq/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/isoseq/tree/master/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/isoseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml new file mode 100644 index 0000000..e2833ee --- /dev/null +++ b/.github/actions/get-shards/action.yml @@ -0,0 +1,69 @@ +name: "Get number of shards" +description: "Get the number of nf-test shards for the current CI job" +inputs: + max_shards: + description: "Maximum number of shards allowed" + required: true + paths: + description: "Component paths to test" + required: false + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +outputs: + shard: + description: "Array of shard numbers" + value: ${{ steps.shards.outputs.shard }} + total_shards: + description: "Total number of shards" + value: ${{ steps.shards.outputs.total_shards }} +runs: + using: "composite" + steps: + - name: Install nf-test + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + with: + version: ${{ env.NFT_VER }} + - name: Get number of shards + id: shards + shell: bash + run: | + # Run nf-test with dynamic parameter + nftest_output=$(nf-test test \ + --profile +docker \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --dry-run \ + --ci \ + --changed-since HEAD^) || { + echo "nf-test command failed with exit code $?" + echo "Full output: $nftest_output" + exit 1 + } + echo "nf-test dry-run output: $nftest_output" + + # Default values for shard and total_shards + shard="[]" + total_shards=0 + + # Check if there are related tests + if echo "$nftest_output" | grep -q 'No tests to execute'; then + echo "No related tests found." + else + # Extract the number of related tests + number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') + if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then + shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) + shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) + total_shards="$shards_to_run" + else + echo "Unexpected output format. Falling back to default values." + fi + fi + + # Write to GitHub Actions outputs + echo "shard=$shard" >> $GITHUB_OUTPUT + echo "total_shards=$total_shards" >> $GITHUB_OUTPUT + + # Debugging output + echo "Final shard array: $shard" + echo "Total number of shards: $total_shards" diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml new file mode 100644 index 0000000..4175e3c --- /dev/null +++ b/.github/actions/nf-test/action.yml @@ -0,0 +1,111 @@ +name: "nf-test Action" +description: "Runs nf-test with common setup steps" +inputs: + profile: + description: "Profile to use" + required: true + shard: + description: "Shard number for this CI job" + required: true + total_shards: + description: "Total number of test shards(NOT the total number of matrix jobs)" + required: true + paths: + description: "Test paths" + required: true + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: false +runs: + using: "composite" + steps: + - name: Setup Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 + with: + version: "${{ env.NXF_VERSION }}" + + - name: Set up Python + uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 + with: + python-version: "3.14" + + - name: Install nf-test + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 + with: + version: "${{ env.NFT_VER }}" + install-pdiff: true + + - name: Setup apptainer + if: contains(inputs.profile, 'singularity') + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0 + + - name: Set up Singularity + if: contains(inputs.profile, 'singularity') + shell: bash + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Conda setup + if: contains(inputs.profile, 'conda') + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 + with: + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge + channel-priority: strict + conda-remove-defaults: true + + - name: Run nf-test + shell: bash + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + run: | + nf-test test \ + --profile=+${{ inputs.profile }} \ + $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \ + --ci \ + --changed-since HEAD^ \ + --verbose \ + --tap=test.tap \ + --shard ${{ inputs.shard }}/${{ inputs.total_shards }} + + # Save the absolute path of the test.tap file to the output + echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT + + - name: Generate test summary + if: always() + shell: bash + run: | + # Add header if it doesn't exist (using a token file to track this) + if [ ! -f ".summary_header" ]; then + echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY + echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY + touch .summary_header + fi + + if [ -f test.tap ]; then + while IFS= read -r line; do + if [[ $line =~ ^ok ]]; then + test_name="${line#ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + elif [[ $line =~ ^not\ ok ]]; then + test_name="${line#not ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + done < test.tap + else + echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + + - name: Clean up + if: always() + shell: bash + run: | + sudo rm -rf /home/ubuntu/tests/ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index aa7237c..96d1937 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,40 +1,64 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the main/master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: + workflow_dispatch: + pull_request_review: + types: [submitted] release: types: [published] - workflow_dispatch: + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/isoseq' + # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered + if: github.repository == 'nf-core/isoseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release' runs-on: ubuntu-latest steps: - - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 - # TODO nf-core: You can customise AWS full pipeline tests as required - # Add full size test data (but still relatively small datasets for few samples) - # on the `test_full.config` test runs with only one set of parameters + - name: Set revision variable + id: revision + run: | + echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" + - name: Launch workflow via Seqera Platform + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/isoseq/work-${{ github.sha }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} + revision: ${{ steps.revision.outputs.revision }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/isoseq/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'isoseq' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *isoseq/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *isoseq/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/isoseq/results-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/isoseq/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index e4980e3..67d23c0 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,22 +12,22 @@ jobs: steps: # Launch workflow using Seqera Platform CLI tool action - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/isoseq/work-${{ github.sha }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/isoseq/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/isoseq/results-test-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/isoseq/results-test-${{ github.sha }}" } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 3d40ebb..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,47 +0,0 @@ -name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors -on: - push: - branches: - - dev - pull_request: - release: - types: [published] - -env: - NXF_ANSI_LOG: false - -concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true - -jobs: - test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/isoseq') }}" - runs-on: ubuntu-latest - strategy: - matrix: - NXF_VER: - - "23.04.0" - - "latest-everything" - steps: - - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - name: Run pipeline with test data (uLTRA) - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results - - - name: Run pipeline with test data (minimap2) - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_minimap2,docker --outdir ./results diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 0b6b1f2..b694012 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d64..ca2eb82 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,86 +1,142 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: - types: - - opened - - edited - - synchronize - branches: - - master - pull_request_target: branches: + - main - master env: NXF_ANSI_LOG: false jobs: + configure: + runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + download: runs-on: ubuntu-latest + needs: configure steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: - python-version: "3.12" + python-version: "3.14" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 + + - name: Read .nf-core.yml + id: read_yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Get the repository name and current branch set as environment variable + - name: Make a cache directory for the container images run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + mkdir -p ./singularity_container_images - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" + + - name: Compare container image counts + id: count_comparison + run: | + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml similarity index 71% rename from .github/workflows/fix-linting.yml rename to .github/workflows/fix_linting.yml index 0e22ff2..8da3b4e 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,13 +13,13 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} # indication that the linting is being fixed - name: React on comment - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: eyes @@ -31,30 +31,26 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.12" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + if: steps.prek.outcome == 'success' + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: "+1" - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" @@ -67,21 +63,21 @@ jobs: - name: react if linting errors were fixed id: react-if-fixed if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: hooray - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: confused - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: issue-number: ${{ github.event.issue.number }} body: | diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index c88fcbf..277f12f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,11 +1,8 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: - push: - branches: - - dev pull_request: release: types: [published] @@ -14,46 +11,55 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.12" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: - python-version: "3.12" + python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Run nf-core lint + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: | - cd ${GITHUB_WORKSPACE} - nf-core lint --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} @@ -61,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 0000000..e363215 --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,201 @@ +name: Run nf-test +on: + pull_request: + paths-ignore: + - "docs/**" + - "**/meta.yml" + - "**/*.md" + - "**/*.png" + - "**/*.svg" + release: + types: [published] + workflow_dispatch: + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + NFT_VER: "0.9.4" + NFT_WORKDIR: "~" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + +jobs: + nf-test-changes: + name: nf-test-changes + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test-changes + - runner=4cpu-linux-x64 + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + fetch-depth: 0 + + - name: get number of shards + id: set-shards + uses: ./.github/actions/get-shards + env: + NFT_VER: ${{ env.NFT_VER }} + with: + max_shards: 7 + + - name: debug + run: | + echo ${{ steps.set-shards.outputs.shard }} + echo ${{ steps.set-shards.outputs.total_shards }} + + nf-test: + name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" + needs: [nf-test-changes] + if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-nf-test + - runner=4cpu-linux-x64 + strategy: + fail-fast: false + matrix: + shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} + profile: [conda, docker, singularity] + isMain: + - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} + # Exclude conda and singularity on dev + exclude: + - isMain: false + profile: "conda" + - isMain: false + profile: "singularity" + NXF_VER: + - "25.10.4" + - "latest-everything" + env: + NXF_ANSI_LOG: false + TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} + + steps: + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + fetch-depth: 0 + + - name: Run nf-test + id: run_nf_test + uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} + env: + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} + with: + profile: ${{ matrix.profile }} + shard: ${{ matrix.shard }} + total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + + # continue-on-error keeps latest-everything from failing the job, so it never shows up in + # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead; + # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those. + - name: Prepare PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + run: | + mkdir -p pr-comment-fragment + echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md + + - name: Upload PR comment fragment + if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment-fragment-${{ strategy.job-index }} + path: pr-comment-fragment/ + + confirm-pass: + needs: [nf-test] + if: always() + runs-on: # use self-hosted runners + - runs-on=${{ github.run_id }}-confirm-pass + - runner=2cpu-linux-x64 + steps: + - name: One or more tests failed (excluding latest-everything) + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "::group::DEBUG: `needs` Contents" + echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" + echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" + echo "::endgroup::" + + - name: Download PR comment fragments + if: ${{ always() }} + uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + continue-on-error: true + with: + pattern: pr-comment-fragment-* + path: pr-comment-fragments + merge-multiple: true + + # Build a comment for the shared pr-comment.yml poster to publish on the PR. + # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported. + - name: Prepare PR comment + if: ${{ always() }} + env: + PR_NUMBER: ${{ github.event.pull_request.number }} + RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "nf-test" > pr-comment/header.txt + if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then + { + echo "## ❌ nf-test failed with latest Nextflow version" + echo "" + echo "> [!NOTE]" + echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure." + echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing." + echo "" + cat pr-comment-fragments/*.md + echo "" + echo "See the [full run](${RUN_URL}) for details." + } > pr-comment/comment.md + fi + + - name: Upload PR comment artifact + if: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf..4974f44 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,9 +12,13 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - name: get description + id: get_description + run: | + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT + - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6 with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -22,48 +26,15 @@ jobs: # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - + ${{ steps.get_description.outputs.description }} Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml new file mode 100644 index 0000000..149e285 --- /dev/null +++ b/.github/workflows/template-version-comment.yml @@ -0,0 +1,60 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: + pull_request: + +permissions: {} + +jobs: + check_template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core + + - name: Build PR comment if template is outdated + # The fork-controlled version is passed via the environment and only ever + # used as quoted shell data (never interpolated into a command), so it + # cannot be used for script injection. + env: + PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }} + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + mkdir -p pr-comment + echo "$PR_NUMBER" > pr-comment/pr_number.txt + echo "template-version" > pr-comment/header.txt + + latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1) + + if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then + cat > pr-comment/comment.md < [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). + EOF + fi + + - name: Upload PR comment artifact + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.gitignore b/.gitignore index 2503c16..cc2b1a7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,3 @@ -assets/long_reads.fa.gz .nextflow* work/ data/ @@ -7,5 +6,5 @@ results/ testing/ testing* *.pyc -.idea/ -.vscode +null/ +.lineage/ diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 105a182..0000000 --- a/.gitpod.yml +++ /dev/null @@ -1,20 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS - -vscode: - extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 0000000..e9ba4f9 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index b2a1c59..a846008 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,8 +1,16 @@ +nf_core_version: 4.1.0 repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: "Sébastien Guizard (@sguizard)" + description: Genes and transcripts annotation with Isoseq using uLTRA and TAMA + force: false + is_nfcore: true + name: isoseq + org: nf-core + outdir: . + version: 3.0.0 lint: files_unchanged: - - ".github/workflows/linting.yml" - - .github/workflows/branch.yml - files_exist: - - .github/workflows/linting_comment.yml + - assets/nf-core-isoseq_logo_light.png + - docs/images/nf-core-isoseq_logo_light.png + - docs/images/nf-core-isoseq_logo_dark.png diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1d..e9503db 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,10 +4,47 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.2.5 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + - prettier@3.9.6 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 hooks: - - id: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/(?!local/).*| + subworkflows/(?!local/).*| + .*\.snap$ + )$ + - id: end-of-file-fixer + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/(?!local/).*| + subworkflows/(?!local/).*| + .*\.snap$ + )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/.prettierignore b/.prettierignore index 437d763..63cde50 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ @@ -10,3 +8,7 @@ testing/ testing* *.pyc bin/ +.nf-test/ +ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/.prettierrc.yml b/.prettierrc.yml index c81f9a7..07dbd8b 100644 --- a/.prettierrc.yml +++ b/.prettierrc.yml @@ -1 +1,6 @@ printWidth: 120 +tabWidth: 4 +overrides: + - files: "*.{md,yml,yaml,html,css,scss,js,cff}" + options: + tabWidth: 2 diff --git a/CHANGELOG.md b/CHANGELOG.md index b4de61a..e21e9af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,78 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.0.0 - Patchwork Zooble [07/08/2026] + +> [!WARNING] +> This is a major release with breaking changes. Samplesheets and command lines written for +> v2.0.0 will not work unmodified. See the migration notes below. + +### `Added` + +- New samplesheet-driven input system: each row declares its own entry point via `start_from`, + allowing subreads, CCS, full-length and long-read FASTA inputs to be mixed in a single run + [#40](https://github.com/nf-core/isoseq/issues/40), [#57](https://github.com/nf-core/isoseq/issues/57) +- Support for multiple libraries (cells) per sample, merged with TAMA +- Input chunking before mapping via the new `chunker` subworkflow, controlled by `chunk_ccs` + and `chunk_mapping` +- Added parameter `tama_merge_all` to allow merging of sample-wise beds into a single annotation bed +- Updated nf-core template to version 4.1.0 + +### `Changed` + +- **Breaking:** the samplesheet format has been redefined. Columns are now + `sample,seq_data,pbi,start_from`, replacing `sample,bam,pbi,reads`. The `seq_data` column + takes any supported input file, and `start_from` (`ccs`, `lima`, `refine` or `mapping`) + declares where that row enters the pipeline. The `None` placeholder is replaced by `none` + for absent `pbi` files. +- **Breaking:** the `chunk` parameter has been split into `chunk_ccs` and `chunk_mapping`, + which independently control chunking of CCS generation and of mapping. +- Software versions are now collected through Nextflow topic channels instead of a dedicated + module. +- `--primers` is no longer unconditionally required. It is only consumed by `LIMA` and + `isoseq refine`, so it is now required only when at least one samplesheet row uses + `start_from` `ccs`, `lima` or `refine`. Runs where every row uses `mapping` can omit it + [#50](https://github.com/nf-core/isoseq/issues/50) + +### `Removed` + +- **Breaking:** removed the `--entrypoint` parameter. Per-row `start_from` in the samplesheet + replaces it, and is strictly more flexible: entry points can now differ between samples + within one run. +- **Breaking:** removed `--max_cpus`, `--max_memory` and `--max_time`. These were replaced by + the `resourceLimits` directive in the nf-core template; set limits in a custom config instead. +- Removed the `--hook_url` parameter, following the nf-core template. +- Removed the `custom/dumpsoftwareversions` module. + +### `Fixed` + +- Updated all nf-core modules to their latest revisions (`bamtools/convert`, `gnu/sort`, + `gstama/collapse`, `gstama/merge`, `gstama/polyacleanup`, `gunzip`, `isoseq/refine`, `lima`, + `minimap2/align`, `multiqc`, `pbccs`, `ultra/align`, `ultra/index`) +- Replaced the `utils_nfvalidation_plugin` subworkflow with `utils_nfschema_plugin`, moving + parameter validation to `nf-schema` 2.5.1 +- Moved local subworkflows into their own directories to follow nf-core guidelines +- Improved samplesheet validation: `start_from` is now an `enum`, file-extension patterns are + correctly anchored, and a `.bam.pbi` index is required when `start_from` is `ccs` + [#48](https://github.com/nf-core/isoseq/issues/48) +- Fixed `CSS` / `CCS` typo in the documentation [#36](https://github.com/nf-core/isoseq/issues/36) +- Removed a vulnerable artifact pattern from the PR-comment workflow + [#61](https://github.com/nf-core/isoseq/pull/61) + +### `Dependencies` + +| Tool | Previous version | New version | +| --------- | ---------------- | ----------- | +| coreutils | 9.3 | 9.5 | +| lima | 2.9.0 | 2.12.0 | +| minimap2 | 2.28 | 2.30 | +| multiqc | 1.24.1 | 1.35 | +| samtools | 1.20 | 1.23.1 | + +### `Deprecated` + +- None + ## v2.0.0 - Sapphire Duck [05/09/2024] New entrypoint option to skip isoseq pre-processing. @@ -48,16 +120,16 @@ Update the pipeline to nf-core 2.9. - Add gnu/sort to sort annotation before uLTRA index - Update citations - Add background to pipeline png - | Tool | Previous version | New version | - | ----------------------- | ---------------- | ----------- | - | isoseq3 | 3.8.1 | 3.8.2 | - | lima | 2.6.0 | 2.7.1 | - | bamtools/convert | 2.5.1 | 2.5.2 | - | gstama/merge | 1.0.2 | 1.0.3 | - | uLTRA/index | 0.0.4.2 | 0.1 | - | uLTRA/align | 0.0.4.2 | 0.1 | - | samtools | 1.17 | 1.17 | - | gnu/sort | ---- | 8.25 | + | Tool | Previous version | New version | + | ---------------- | ---------------- | ----------- | + | isoseq3 | 3.8.1 | 3.8.2 | + | lima | 2.6.0 | 2.7.1 | + | bamtools/convert | 2.5.1 | 2.5.2 | + | gstama/merge | 1.0.2 | 1.0.3 | + | uLTRA/index | 0.0.4.2 | 0.1 | + | uLTRA/align | 0.0.4.2 | 0.1 | + | samtools | 1.17 | 1.17 | + | gnu/sort | ---- | 8.25 | ### `Dependencies` diff --git a/CITATIONS.md b/CITATIONS.md index ba9c0dd..c010a82 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -36,11 +36,9 @@ > Kuo, R.I., Cheng, Y., Zhang, R. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 21, 751 (2020). - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -60,6 +58,6 @@ > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. -- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) +- [Singularity / Apptainer](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/LICENSE b/LICENSE index 4b9d949..da41bc4 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Sébastien Guizard (@sguizard) +Copyright (c) The nf-core/isoseq team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index b989d74..cef920e 100644 --- a/README.md +++ b/README.md @@ -5,25 +5,26 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/isoseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/isoseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/isoseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7116979-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7116979) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/isoseq) +[![GitHub Actions CI Status](https://github.com/nf-core/isoseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/nf-test.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/isoseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/isoseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13694618-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13694618) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/isoseq/results) -[![DOI](https://zenodo.org/badge/499464196.svg)](https://zenodo.org/badge/latestdoi/499464196) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7116979-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7116979) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/isoseq) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23isoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/isoseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23isoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/isoseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction **nf-core/isoseq** is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Starting from raw isoseq subreads, the pipeline: -- Generates the Circular Consensus Sequences (CSS) +- Generates the Circular Consensus Sequences (CCS) - Clean and polish CCS to create Full Length Non Chimeric (FLNC) reads @@ -39,8 +40,8 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Pipeline summary -1. Generate CCS consensuses from raw isoseq subreads ([`PBCCS`](https://github.com/PacificBiosciences/ccs)) -2. Remove primer sequences from consensuses ([`LIMA`](https://github.com/pacificbiosciences/barcoding/)) +1. Generate CCS consensuses from raw isoseq subreads (Optional, [`PBCCS`](https://github.com/PacificBiosciences/ccs)) +2. Remove primer sequences from consensuses (Optional, [`LIMA`](https://github.com/pacificbiosciences/barcoding/)) 3. Detect and remove chimeric reads ([`ISOSEQ3 REFINE`](https://github.com/PacificBiosciences/IsoSeq)) 4. Convert bam file into fasta file ([`BAMTOOLS CONVERT`](https://github.com/pezmaster31/bamtools)) 5. Select reads with a polyA tail and trim it ([`GSTAMA_POLYACLEANUP`](https://github.com/GenomeRIK/tama)) @@ -53,18 +54,22 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv -sample,bam,pbi,reads -sample1,sample1.subreads.bam,sample1.subreads.bam.pbi,None +sample,seq_data,pbi,start_from +sample1,sample1.subreads.bam,sample1.subreads.bam.pbi,ccs +sample2,sample2.ccs.bam,none,lima +sample3,sample3.fl.primer_5p--primer_3p.bam,none,refine +sample4,sample4.long_reads.fa.gz,none,mapping ``` -Each row represents a pair of raw subreads and it's associated pacbio index (pbi) file fastq files. +The file list all datasets to analyse. Those datasets can be raw subreads, Circular Consensus Sequences (CCS), Full Length sequences produced by LIMA (Pacbio software suite), or long reads sequence Pacbio Hifi (or Oxford Nanopore long reads!) +The first column define the sample ID, the second sequence data file, the third PacBio Index file (subreads only) and the program where to start the analysis. Now, you can run the pipeline using: @@ -78,8 +83,7 @@ nextflow run nf-core/isoseq \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/isoseq/usage) and the [parameter documentation](https://nf-co.re/isoseq/parameters). @@ -103,12 +107,13 @@ We thank the following people for their extensive assistance in the development - The nf-core community for their help in the development of this pipeline - [James A. Fellows Yates](https://github.com/jfy133) & nf-core for the metro map style components for pipeline graph - [Júlia Mir Pedrol](https://github.com/mirpedrol) for debugging help +- [Usman Rashid](https://github.com/GallVp) for his contributions on pipeline development This pipeline has been developed as part of the GENE-SWitCH project. This project has received funding from the European Union's Horizon 2020 Research and Innovation Programme under the grant agreement n° 817998. ## Contributions and Support -If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). +If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#isoseq` channel](https://nfcore.slack.com/channels/isoseq) (you can join with [this invite](https://nf-co.re/join/slack)). diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json deleted file mode 100644 index 0d5154a..0000000 --- a/assets/adaptivecard.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - "type": "message", - "attachments": [ - { - "contentType": "application/vnd.microsoft.card.adaptive", - "contentUrl": null, - "content": { - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "msteams": { - "width": "Full" - }, - "type": "AdaptiveCard", - "version": "1.2", - "body": [ - { - "type": "TextBlock", - "size": "Large", - "weight": "Bolder", - "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/isoseq v${version} - ${runName}", - "wrap": true - }, - { - "type": "TextBlock", - "spacing": "None", - "text": "Completed at ${dateComplete} (duration: ${duration})", - "isSubtle": true, - "wrap": true - }, - { - "type": "TextBlock", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", - "wrap": true - }, - { - "type": "TextBlock", - "text": "The command used to launch the workflow was as follows:", - "wrap": true - }, - { - "type": "TextBlock", - "text": "${commandLine}", - "isSubtle": true, - "wrap": true - } - ], - "actions": [ - { - "type": "Action.ShowCard", - "title": "Pipeline Configuration", - "card": { - "type": "AdaptiveCard", - "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", - "body": [ - { - "type": "FactSet", - "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> - ] - } - ] - } - } - ] - } - } - ] -} diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index cce31e5..0bf4411 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/isoseq Methods Description" section_href: "https://github.com/nf-core/isoseq" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

Data was processed using nf-core/isoseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 61a8541..47190c7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/isoseq analysis pipeline. For information about how to interpret - these results, please see the documentation. - + This report has been generated by the nf-core/isoseq + analysis pipeline. For information about how to interpret these results, please see the + documentation. report_section_order: "nf-core-isoseq-methods-description": order: -1000 diff --git a/assets/nf-core-isoseq_logo_light.png b/assets/nf-core-isoseq_logo_light.png index a1ac089..57cac45 100644 Binary files a/assets/nf-core-isoseq_logo_light.png and b/assets/nf-core-isoseq_logo_light.png differ diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv deleted file mode 100644 index cd01ecd..0000000 --- a/assets/samplesheet.csv +++ /dev/null @@ -1,3 +0,0 @@ -sample,bam,pbi -sample1,sample1.subreads.bam,sample1.subreads.bam.pbi -sample2,sample2.subreads.bam,sample2.subreads.bam.pbi diff --git a/assets/samplesheet_map_entrypoint.csv b/assets/samplesheet_map_entrypoint.csv deleted file mode 100644 index a6514c6..0000000 --- a/assets/samplesheet_map_entrypoint.csv +++ /dev/null @@ -1,2 +0,0 @@ -sample,bam,pbi,reads -alz,None,None,/home/sguizard/Work/Dev/github/nf-core/isoseq/assets/long_reads.fa.gz diff --git a/assets/samplesheet_v2_ccs_lima_refine_map.csv b/assets/samplesheet_v2_ccs_lima_refine_map.csv new file mode 100644 index 0000000..6d210fe --- /dev/null +++ b/assets/samplesheet_v2_ccs_lima_refine_map.csv @@ -0,0 +1,5 @@ +sample,seq_data,pbi,start_from +sample1,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz.1perc.subreads.10000.bam,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz.1perc.subreads.10000.bam.pbi,ccs +sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam,none,lima +sample3,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz_lima.fl.NEB_5p--NEB_Clontech_3p.bam,none,refine +sample4,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/long_reads.fa.gz,none,mapping diff --git a/assets/samplesheet_v2_ccs_map.csv b/assets/samplesheet_v2_ccs_map.csv new file mode 100644 index 0000000..73b33a4 --- /dev/null +++ b/assets/samplesheet_v2_ccs_map.csv @@ -0,0 +1,3 @@ +sample,seq_data,pbi,start_from +sample1,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz.1perc.subreads.10000.bam,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz.1perc.subreads.10000.bam.pbi,ccs +sample4,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/long_reads.fa.gz,none,mapping diff --git a/assets/samplesheet_v2_lima_refine_map.csv b/assets/samplesheet_v2_lima_refine_map.csv new file mode 100644 index 0000000..0936775 --- /dev/null +++ b/assets/samplesheet_v2_lima_refine_map.csv @@ -0,0 +1,4 @@ +sample,seq_data,pbi,start_from +sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam,none,lima +sample3,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/assets/alz_lima.fl.NEB_5p--NEB_Clontech_3p.bam,none,refine +sample4,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/long_reads.fa.gz,none,mapping diff --git a/assets/samplesheet_v2_map.csv b/assets/samplesheet_v2_map.csv new file mode 100644 index 0000000..d3da2e9 --- /dev/null +++ b/assets/samplesheet_v2_map.csv @@ -0,0 +1,2 @@ +sample,seq_data,pbi,start_from +sample4,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/long_reads.fa.gz,none,mapping diff --git a/assets/samplesheet_v2_refine_map.csv b/assets/samplesheet_v2_refine_map.csv new file mode 100644 index 0000000..9b3aa23 --- /dev/null +++ b/assets/samplesheet_v2_refine_map.csv @@ -0,0 +1,3 @@ +sample,seq_data,pbi,start_from +sample3,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/alz_lima.fl.NEB_5p--NEB_Clontech_3p.bam,none,refine +sample4,https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/long_reads.fa.gz,none,mapping diff --git a/assets/schema_input.json b/assets/schema_input.json index 48d23fb..3564021 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/isoseq/master/assets/schema_input.json", "title": "nf-core/isoseq pipeline - params.input schema", "description": "Schema for the file provided with params.input", @@ -13,28 +13,52 @@ "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] }, - "bam": { + "seq_data": { "type": "string", + "pattern": "^\\S+\\.(bam|fa|fa\\.gz)$", "format": "file-path", - "exists": false, - "pattern": "(^\\S+\\.bam$|^None$)", - "errorMessage": "Subreads BAM file must be provided, cannot contain spaces and must have extension '.bam' or being 'None' if the entrypoint is 'map'" + "errorMessage": "Sequence data file must be provided, cannot contain spaces and must have extension '.bam', '.fa' or '.fa.gz'" }, "pbi": { - "type": "string", - "format": "file-path", - "exists": false, - "pattern": "(^\\S+\\.bam\\.pbi$|^None$)", - "errorMessage": "PacBio Index file for BAM subreads cannot contain spaces and must have extension '.bam.pbi' or being 'None' if the entrypoint is 'map'" + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+\\.bam\\.pbi$", + "format": "file-path" + }, + { + "type": "string", + "pattern": "^none$" + } + ], + "errorMessage": "PacBio index for a subreads BAM must have extension '.bam.pbi' and cannot contain spaces. Use 'none' when no index applies." }, - "reads": { + "start_from": { "type": "string", - "format": "file-path", - "exists": false, - "pattern": "(^\\S+\\.fa\\.gz$|^None$)", - "errorMessage": "Long reads file cannot contain spaces and must have extension '.bam.pbi' or being 'None' if the entrypoint is 'isoseq'" + "enum": ["ccs", "lima", "refine", "mapping"], + "errorMessage": "start_from must be one of: ccs, lima, refine, mapping", + "meta": ["start_from"] } }, - "required": ["sample"] + "required": ["sample", "seq_data", "start_from"], + "allOf": [ + { + "if": { + "properties": { + "start_from": { "const": "ccs" } + }, + "required": ["start_from"] + }, + "then": { + "required": ["pbi"], + "properties": { + "pbi": { + "pattern": "^\\S+\\.bam\\.pbi$", + "errorMessage": "A PacBio index file ('.bam.pbi') is required when start_from is 'ccs'" + } + } + } + } + ] } } diff --git a/assets/slackreport.json b/assets/slackreport.json deleted file mode 100644 index 042ab1e..0000000 --- a/assets/slackreport.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "attachments": [ - { - "fallback": "Plain-text summary of the attachment.", - "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/isoseq ${version} - ${runName}", - "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", - "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", - "fields": [ - { - "title": "Command used to launch the workflow", - "value": "```${commandLine}```", - "short": false - } - <% - if (!success) { %> - , - { - "title": "Full error message", - "value": "```${errorReport}```", - "short": false - }, - { - "title": "Pipeline configuration", - "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", - "short": false - } - <% } - %> - ], - "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" - } - ] -} diff --git a/conf/base.config b/conf/base.config index 73006d1..7898995 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,45 +10,48 @@ process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } + } + withLabel:process_low_memory { + memory = { 1.GB * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' @@ -57,4 +60,8 @@ process { errorStrategy = 'retry' maxRetries = 2 } + withLabel: process_gpu { + ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } + } } diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config new file mode 100644 index 0000000..eb32fe5 --- /dev/null +++ b/conf/containers_conda_lock_files_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config new file mode 100644 index 0000000..3733ddf --- /dev/null +++ b/conf/containers_conda_lock_files_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config new file mode 100644 index 0000000..ea18c3f --- /dev/null +++ b/conf/containers_docker_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config new file mode 100644 index 0000000..369f743 --- /dev/null +++ b/conf/containers_docker_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config new file mode 100644 index 0000000..932fc7c --- /dev/null +++ b/conf/containers_singularity_https_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config new file mode 100644 index 0000000..4f79532 --- /dev/null +++ b/conf/containers_singularity_https_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config new file mode 100644 index 0000000..2fa065b --- /dev/null +++ b/conf/containers_singularity_oras_amd64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config new file mode 100644 index 0000000..84f0792 --- /dev/null +++ b/conf/containers_singularity_oras_arm64.config @@ -0,0 +1 @@ +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } diff --git a/conf/igenomes.config b/conf/igenomes.config index 3f11437..b8c8154 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -8,433 +8,431 @@ ---------------------------------------------------------------------------------------- */ -params { +params.genomes = [ // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} + 'GRCh37' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt", + mito_name : "MT", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/GRCh37-blacklist.bed", + ], + 'GRCh38' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg38-blacklist.bed", + ], + 'CHM13' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/", + bwamem2 : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/", + gtf : "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf", + gff : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz", + mito_name : "chrM", + ], + 'GRCm38' : [ + 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"${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt", + mito_name : "MT", + ], + 'AGPv3' : [ + fasta : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed", + mito_name : "Mt", + ], + 'hg38' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg38-blacklist.bed", + ], + 'hg19' : [ + fasta : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "2.7e9", + blacklist : "${projectDir}/assets/blacklists/hg19-blacklist.bed", + ], + 'mm10' : [ + fasta : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "1.87e9", + blacklist : "${projectDir}/assets/blacklists/mm10-blacklist.bed", + ], + 'bosTau8' : [ + fasta : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed", + mito_name : "chrM", + ], + 'ce10' : [ + fasta : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "9e7", + ], + 'canFam3' : [ + fasta : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt", + mito_name : "chrM", + ], + 'danRer10' : [ + fasta : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "1.37e9", + ], + 'dm6' : [ + fasta : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed", + mito_name : "chrM", + macs_gsize : "1.2e8", + ], + 'equCab2' : [ + fasta : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt", + mito_name : "chrM", + ], + 'galGal4' : [ + fasta : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt", + mito_name : "chrM", + ], + 'panTro4' : [ + fasta : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt", + mito_name : "chrM", + ], + 'rn6' : [ + fasta : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed", + mito_name : "chrM", + ], + 'sacCer3' : [ + fasta : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/", + readme : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt", + mito_name : "chrM", + macs_gsize : "1.2e7", + ], + 'susScr3' : [ + fasta : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa", + bwa : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/", + bowtie2 : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/", + star : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/", + bismark : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/", + gtf : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf", + bed12 : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed", + readme : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt", + mito_name : "chrM", + ], +] diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 0000000..b4034d8 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index 96d5ae1..661a0ff 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -107,23 +107,15 @@ process { ext.args = "--isoseq" } - if (params.capped == true) { - withName: GSTAMA_COLLAPSE { - publishDir = [ - path: { "${params.outdir}/07_GSTAMA_COLLAPSE" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - ext.args = "-x capped -b BAM -a ${params.five_prime} -m ${params.splice_junction} -z ${params.three_prime}" - } - } else { - withName: GSTAMA_COLLAPSE { - publishDir = [ - path: { "${params.outdir}/07_GSTAMA_COLLAPSE" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - ext.args = "-x no_cap -b BAM -a ${params.five_prime} -m ${params.splice_junction} -z ${params.three_prime}" + withName: GSTAMA_COLLAPSE { + publishDir = [ + path: { "${params.outdir}/07_GSTAMA_COLLAPSE" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + ext.args = { + def cap_flag = params.capped ? 'capped' : 'no_cap' + "-x ${cap_flag} -b BAM -a ${params.five_prime} -m ${params.splice_junction} -z ${params.three_prime}" } } @@ -144,20 +136,4 @@ process { ext.args = "-a ${params.five_prime} -m ${params.splice_junction} -z ${params.three_prime}" } - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - } diff --git a/conf/test.config b/conf/test.config index 491a9a6..129d574 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,22 +10,26 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet.csv' - primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta' - fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' - gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf' + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + gtf = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf' rq = 0.9 - chunk = 5 + chunk_ccs = 5 + chunk_mapping = 500 five_prime = 100 splice_junction = 10 three_prime = 100 diff --git a/conf/test_full.config b/conf/test_full.config index 0302104..c0c4088 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,10 +15,11 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet_full.csv' - primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers_complete.fasta' + input = params.pipelines_testdata_base_path + 'samplesheet_v2_full.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers_complete.fasta' rq = 0.9 - chunk = 100 + chunk_ccs = 100 + chunk_mapping = 100000 five_prime = 100 splice_junction = 10 three_prime = 100 diff --git a/conf/test_minimap2.config b/conf/test_minimap2.config index fe07514..225bb5b 100644 --- a/conf/test_minimap2.config +++ b/conf/test_minimap2.config @@ -10,21 +10,25 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile - Minimap2 path' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet.csv' - primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta' - fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' rq = 0.9 - chunk = 5 + chunk_ccs = 5 + chunk_mapping = 500 five_prime = 100 splice_junction = 10 three_prime = 100 diff --git a/conf/test_minimap2_map_entrypoint.config b/conf/test_samplesheet_v2_ccs.config similarity index 55% rename from conf/test_minimap2_map_entrypoint.config rename to conf/test_samplesheet_v2_ccs.config index 7c11013..43ba727 100644 --- a/conf/test_minimap2_map_entrypoint.config +++ b/conf/test_samplesheet_v2_ccs.config @@ -10,26 +10,28 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { - config_profile_name = 'Test profile - Minimap2 path - Entrypoint map' + config_profile_name = 'Test inputs ccs' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet_map_entrypoint.csv' - primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta' - fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' - - chunk = 100 + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 five_prime = 100 splice_junction = 10 three_prime = 100 capped = true - aligner = 'minimap2' - entrypoint = 'map' } diff --git a/conf/test_samplesheet_v2_ccs_lima_refine_map.config b/conf/test_samplesheet_v2_ccs_lima_refine_map.config new file mode 100644 index 0000000..8f0415a --- /dev/null +++ b/conf/test_samplesheet_v2_ccs_lima_refine_map.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs ccs lima refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs_lima_refine_map.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_ccs_lima_refine_map_mergeAll.config b/conf/test_samplesheet_v2_ccs_lima_refine_map_mergeAll.config new file mode 100644 index 0000000..16219a8 --- /dev/null +++ b/conf/test_samplesheet_v2_ccs_lima_refine_map_mergeAll.config @@ -0,0 +1,38 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs ccs lima refine map and merge all samples' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs_lima_refine_map.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' + tama_merge_all = true +} diff --git a/conf/test_samplesheet_v2_ccs_map.config b/conf/test_samplesheet_v2_ccs_map.config new file mode 100644 index 0000000..90fe6e2 --- /dev/null +++ b/conf/test_samplesheet_v2_ccs_map.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs ccs map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_ccs_map.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 55 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_lima.config b/conf/test_samplesheet_v2_lima.config new file mode 100644 index 0000000..21d9782 --- /dev/null +++ b/conf/test_samplesheet_v2_lima.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs lima refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_lima.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_lima_refine_map.config b/conf/test_samplesheet_v2_lima_refine_map.config new file mode 100644 index 0000000..e744b99 --- /dev/null +++ b/conf/test_samplesheet_v2_lima_refine_map.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs lima refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_lima_refine_map.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_map.config b/conf/test_samplesheet_v2_map.config new file mode 100644 index 0000000..e881a73 --- /dev/null +++ b/conf/test_samplesheet_v2_map.config @@ -0,0 +1,40 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + // NOTE: `primers` is deliberately omitted. Every row of samplesheet_v2_map.csv uses + // start_from 'mapping', so LIMA and ISOSEQ_REFINE never run and no primer file is + // needed. This profile is the regression test for + // https://github.com/nf-core/isoseq/issues/50 - do not add `primers` back. + input = params.pipelines_testdata_base_path + 'samplesheet_v2_map.csv' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 55 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_multi_lib.config b/conf/test_samplesheet_v2_multi_lib.config new file mode 100644 index 0000000..8bad7c1 --- /dev/null +++ b/conf/test_samplesheet_v2_multi_lib.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs ccs lima refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_multi_lib.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 500 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_refine.config b/conf/test_samplesheet_v2_refine.config new file mode 100644 index 0000000..5f2e105 --- /dev/null +++ b/conf/test_samplesheet_v2_refine.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_refine.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 55 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_samplesheet_v2_refine_map.config b/conf/test_samplesheet_v2_refine_map.config new file mode 100644 index 0000000..9df2dc1 --- /dev/null +++ b/conf/test_samplesheet_v2_refine_map.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/isoseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test inputs refine map' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'samplesheet_v2_refine_map.csv' + primers = params.pipelines_testdata_base_path + 'testdata/primers.fasta' + fasta = params.pipelines_testdata_base_path + 'reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' + rq = 0.9 + chunk_ccs = 5 + chunk_mapping = 55 + five_prime = 100 + splice_junction = 10 + three_prime = 100 + capped = true + aligner = 'minimap2' +} diff --git a/conf/test_ultra_map_entrypoint.config b/conf/test_ultra_map_entrypoint.config deleted file mode 100644 index 0ac7c19..0000000 --- a/conf/test_ultra_map_entrypoint.config +++ /dev/null @@ -1,36 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/isoseq -profile test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'Test profile - ULTRA path - Entrypoint map' - config_profile_description = 'Minimal test dataset to check pipeline function' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - - // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet_map_entrypoint.csv' - primers = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta' - fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta' - gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf' - - chunk = 100 - five_prime = 100 - splice_junction = 10 - three_prime = 100 - capped = true - - aligner = 'ultra' - entrypoint = 'map' -} diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md new file mode 100644 index 0000000..8dfad3d --- /dev/null +++ b/docs/CONTRIBUTING.md @@ -0,0 +1,185 @@ +--- +title: Contributing +markdownPlugin: checklist +--- + +# `nf-core/isoseq`: Contributing guidelines + +Hi there! +Thanks for taking an interest in improving nf-core/isoseq. + +This page describes the recommended nf-core way to contribute to both nf-core/isoseq and nf-core pipelines in general, including: + +- [General contribution guidelines](#general-contribution-guidelines): common procedures or guides across all nf-core pipelines. +- [Pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): procedures or guides specific to the development conventions of nf-core/isoseq. + +> [!NOTE] +> If you need help using or modifying nf-core/isoseq, ask on the nf-core Slack [#isoseq](https://nfcore.slack.com/channels/isoseq) channel ([join our Slack here](https://nf-co.re/join/slack)). + +## General contribution guidelines + +### Contribution quick start + +To contribute code to any nf-core pipeline: + +- [ ] Ensure you have Nextflow, nf-core tools, and nf-test installed. See the [nf-core/tools repository](https://github.com/nf-core/tools) for instructions. +- [ ] Check whether a GitHub [issue](https://github.com/nf-core/isoseq/issues) about your idea already exists. If an issue does not exist, create one so that others are aware you are working on it. +- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/isoseq repository](https://github.com/nf-core/isoseq) to your GitHub account. +- [ ] Create a branch on your forked repository and make your changes following [pipeline conventions](#pipeline-contribution-conventions) (if applicable). +- [ ] To fix major bugs, name your branch `patch` and follow the [patch release](#patch-release) process. +- [ ] Update relevant documentation within the `docs/` folder, use nf-core/tools to update `nextflow_schema.json`, and update `CITATIONS.md`. +- [ ] Run and/or update tests. See [Testing](#testing) for more information. +- [ ] [Lint](#lint-tests) your code with nf-core/tools. +- [ ] Submit a pull request (PR) against the `dev` branch and request a review. + +If you are not used to this workflow with Git, see the [GitHub documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or [Git resources](https://try.github.io/) for more information. + +## Use of AI and LLMs + +The nf-core stance on the use of AI and LLMs is that humans are still ultimately responsible for their submitted code, regardless of the tools they use. + +If you’re using AI tools, try to stick by these guidelines: + +- Keep PRs as small and focused as possible +- Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR) +- Review all generated code yourself before opening a PR, and ensure that you understand it +- Engage with the community review process and expect to make revisions + +For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team. + +### Getting help + +For further information and help, see the [nf-core/isoseq documentation](https://nf-co.re/isoseq/usage) or ask on the nf-core [#isoseq](https://nfcore.slack.com/channels/isoseq) Slack channel ([join our Slack here](https://nf-co.re/join/slack)). + +### GitHub Codespaces + +You can contribute to nf-core/isoseq without installing a local development environment on your machine by using [GitHub Codespaces](https://github.com/codespaces). + +[GitHub Codespaces](https://github.com/codespaces) is an online developer environment that runs in your browser, complete with VS Code and a terminal. +Most nf-core repositories include a devcontainer configuration, which creates a GitHub Codespaces environment specifically for Nextflow development. +The environment includes pre-installed nf-core tools, Nextflow, and a few other helpful utilities via a Docker container. + +To get started, open the repository in [Codespaces](https://github.com/nf-core/isoseq/codespaces). + +### Testing + +Once you have made your changes, run the pipeline with nf-test to test them locally. +For additional information, use the `--verbose` flag to view the Nextflow console log output. + +```bash +nf-test test --tag test --profile +docker --verbose +``` + +If you have added new functionality, ensure you update the test assertions in the `.nf.test` files in the `tests/` directory. +Update the snapshots with the following command: + +```bash +nf-test test --tag test --profile +docker --verbose --update-snapshots +``` + +When you create a pull request with changes, GitHub Actions will run automatic tests. +Pull requests are typically reviewed when these tests are passing. + +Two types of tests are typically run: + +#### Lint tests + +nf-core has a [set of guidelines](https://nf-co.re/docs/specifications/overview) which all pipelines must follow. +To enforce these, run linting with nf-core/tools: + +```bash +nf-core pipelines lint +``` + +If you encounter failures or warnings, follow the linked documentation printed to screen. +For more information about linting tests, see [nf-core/tools API documentation](https://nf-co.re/docs/nf-core-tools/api_reference/latest/pipeline_lint_tests/actions_awsfulltest). + +#### Pipeline tests + +Each nf-core pipeline should be set up with a minimal set of test data. +GitHub Actions runs the pipeline on this data to ensure it runs through and exits successfully. +If there are any failures then the automated tests fail. +These tests are run with the latest available version of Nextflow and the minimum required version specified in the pipeline code. + +### Patch release + +> [!WARNING] +> Only in the unlikely event of a release that contains a critical bug. + +- [ ] Create a new branch `patch` on your fork based on `upstream/main` or `upstream/master`. +- [ ] Fix the bug and use nf-core/tools to bump the version to the next semantic version, for example, `1.2.3` → `1.2.4`. +- [ ] Open a Pull Request from `patch` directly to `main`/`master` with the changes. + +### Pipeline contribution conventions + +nf-core semi-standardises how you write code and other contributions to make the nf-core/isoseq code and processing logic more understandable for new contributors and to ensure quality. + +#### Add a new pipeline step + +To contribute a new step to the pipeline, follow the general nf-core coding procedure. +Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): + +- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel. +- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `.nf`. +- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`. +- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values). +- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values). +- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow. +- [ ] Perform local tests to validate that the new code works as expected. + - [ ] If applicable, add a new test in the `tests` directory. +- [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. +- [ ] Update any diagrams or pipeline images as necessary. +- [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. +- [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module. +- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`. + +To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines). + +#### Channel naming schemes + +Use the following naming schemes for channels to make the channel flow easier to understand: + +- Initial process channel: `ch_output_from_` +- Intermediate and terminal channels: `ch__for_` + +#### Default parameter values + +Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`. +They should also be documented in the pipeline JSON schema. + +To update `nextflow_schema.json`, run: + +```bash +nf-core pipelines schema build +``` + +The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation. + +#### Default processes resource requirements + +If you write a local module, specify a default set of resource requirements for the process. + +Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`. +Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline. + +nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). +These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. + +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). + +#### Nextflow version bumping + +If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with: + +```bash +nf-core pipelines bump-version --nextflow . +``` + +#### Images and figures guidelines + +If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics). + +## Pipeline specific contribution guidelines + + diff --git a/docs/images/Isoseq_pipeline_metro.eps b/docs/images/Isoseq_pipeline_metro.eps index ab9cb8b..5acd279 100644 --- a/docs/images/Isoseq_pipeline_metro.eps +++ b/docs/images/Isoseq_pipeline_metro.eps @@ -1,10 +1,10 @@ %!PS-Adobe-3.0 EPSF-3.0 -%%Creator: cairo 1.18.0 (https://cairographics.org) -%%CreationDate: Fri May 17 17:21:38 2024 +%%Creator: cairo 1.16.0 (https://cairographics.org) +%%CreationDate: Thu Nov 27 23:05:47 2025 %%Pages: 1 %%DocumentData: Clean7Bit %%LanguageLevel: 3 -%%BoundingBox: 0 1 741 580 +%%BoundingBox: 0 0 783 612 %%EndComments %%BeginProlog 50 dict begin @@ -74,11 +74,9 @@ /Encoding 256 array 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79.148 c 731.117 78.516 730.102 77.113 729.441 75.746 c 728.781 74.383 +729.074 72.23 729.117 68.77 c 729.164 65.312 733.434 63.906 736.039 63.906 + c 737.672 63.906 739.766 64.367 739.973 66.473 c 740.176 68.578 739.973 + 95.07 739.973 95.07 c 747.738 95.07 l h +747.738 63.242 m f +698.992 68.168 m 708.738 68.168 l 708.496 66.293 708 64.957 707.254 64.156 + c 706.508 63.355 705.402 62.957 703.945 62.957 c 701.164 62.957 699.516 + 64.695 698.992 68.168 c 716.453 73.121 m 699.047 73.121 l 699.707 76.77 + 702.156 78.594 706.395 78.594 c 707.68 78.594 708.938 78.41 710.172 78.047 + c 711.406 77.68 712.719 77.203 714.109 76.613 c 714.109 83.281 l 711.258 + 84.465 708.062 85.055 704.52 85.055 c 701.844 85.055 699.496 84.508 697.48 + 83.414 c 695.465 82.32 693.902 80.746 692.793 78.695 c 691.68 76.648 691.125 + 74.23 691.125 71.453 c 691.125 66.867 692.262 63.312 694.539 60.793 c 696.812 + 58.273 700.055 57.016 704.258 57.016 c 712.492 57.016 716.559 62.383 716.453 + 73.121 c f +593.711 58.531 8.027 26.277 re f +593.711 48.285 8.027 6.242 re f +585.09 47.898 m 591.113 47.898 l 570.18 94.258 l 564.633 94.258 l h +585.09 47.898 m f Q Q showpage %%Trailer diff --git a/docs/images/Isoseq_pipeline_metro.png b/docs/images/Isoseq_pipeline_metro.png index 7ddcf64..194e98f 100644 Binary files a/docs/images/Isoseq_pipeline_metro.png and b/docs/images/Isoseq_pipeline_metro.png differ diff --git a/docs/images/Isoseq_pipeline_metro.svg b/docs/images/Isoseq_pipeline_metro.svg index a6ad91c..92cbc11 100644 --- a/docs/images/Isoseq_pipeline_metro.svg +++ b/docs/images/Isoseq_pipeline_metro.svg @@ -5,11 +5,11 @@ version="1.1" id="svg2" xml:space="preserve" - width="988" - height="772" - viewBox="0 0 988 772" + width="1043.5732" + height="815.56598" + viewBox="0 0 1043.5732 815.56598" sodipodi:docname="Isoseq_pipeline_metro.svg" - inkscape:version="1.2.2 (b0a8486541, 2022-12-01)" + inkscape:version="1.4.2 (ebf0e94, 2025-05-08)" inkscape:export-filename="Isoseq_pipeline_metro.png" inkscape:export-xdpi="300" inkscape:export-ydpi="300" @@ -26,14 +26,14 @@ inkscape:pageopacity="0" inkscape:pagecheckerboard="1" showgrid="false" - inkscape:zoom="0.68237637" - inkscape:cx="220.55277" - inkscape:cy="433.04548" + inkscape:zoom="2.5795985" + inkscape:cx="661.34322" + inkscape:cy="344.43344" inkscape:current-layer="svg2" inkscape:showpageshadow="0" inkscape:deskcolor="#505050" inkscape:window-width="1920" - inkscape:window-height="1052" + inkscape:window-height="1112" inkscape:window-x="0" inkscape:window-y="0" inkscape:window-maximized="1" />EntrypointisoseqEntrypointmapGene models cleaningTAMA collapseList files sampleTAMA filelistMerging annotationsTAMA mergeSamplesheetRemoving polyA tailsTAMA polyAcleanupMinimap2gtfReferenceAnnotationIndexinguLTRA indexSortgnu/sortfastaGenomePrimersfastaGene models cleanningTAMA collapseList files sampleTAMA filelistMerging annotationsTAMA mergebedIsoseqAnnotationsRemoving polyA tailsTAMA polyAcleanupCCScsvSamplesheetbampbibampbicsvSamplesheetfa.gzfa.gzUnzip readsgunzipPrimers RemovalLIMAisoseq3 refinebamtools convertMappinguLTRA alignMinimap2MappingfastaGenomeCompute CCSConcatemer RemovalConvert BAM to FASTA + id="path486-0" />uLTRA alignPrimers RemovalLIMACCSCompute CCSisoseq3 refineConcatemer Removalbamtools convertConvert BAM to FASTAcsvPrimersfastabedIsoseq annotations diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e4..0000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb..0000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf..0000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/images/nf-core-isoseq_logo_dark.png b/docs/images/nf-core-isoseq_logo_dark.png index 5b19384..589441d 100644 Binary files a/docs/images/nf-core-isoseq_logo_dark.png and b/docs/images/nf-core-isoseq_logo_dark.png differ diff --git a/docs/images/nf-core-isoseq_logo_light.png b/docs/images/nf-core-isoseq_logo_light.png index fe45ef7..7a55ecb 100644 Binary files a/docs/images/nf-core-isoseq_logo_light.png and b/docs/images/nf-core-isoseq_logo_light.png differ diff --git a/docs/output.md b/docs/output.md index 22e28ee..1b262f8 100644 --- a/docs/output.md +++ b/docs/output.md @@ -18,7 +18,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [GUNZIP](#gunzip) - Decompress FLNC fastas (uLTRA path only) - [ULTRA or MINIMAP2](#ultra-minimap2) - Map FLNCs on genome - [BIOPERL](#bioperl) - Remove spurious alignments (uLTRA path only, [Issue #11](https://github.com/ksahlin/ultra/issues/11)) -- [SAMTOOLS SORT](#samtools-sort) - Sort alignment and convert sam file into bam file - [TAMA FILE LIST](#tama-file-list) - Prepare list file for TAMA collapse - [TAMA COLLAPSE](#tama-collapse) - Clean gene models - [TAMA MERGE](#tama-merge) - Merge all annotations into one for each sample with TAMA merge @@ -126,36 +125,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [`MINIMAP2`](https://github.com/lh3/minimap2) or [`uLTRA`](https://github.com/ksahlin/ultra) aligns reads ont the genome. -### BIOPERL - -
-Output files - -- `06.3_PERL_BIOPERL/` - - `.chunk_filtered.sam`: The aligned reads with spurious alignments removed. - -
- -[BIOPERL](https://bioperl.org/) Some CIGAR string sometimes with a gap (N). This can happen when using GFF file converted to GTF file. See [Issue #11](https://github.com/ksahlin/ultra/issues/11) from uLTRA repo. - -### SAMTOOLS SORT - -
-Output files - -- `07_SAMTOOLS_SORT/` - - `.chunk_sorted.bam`: The sorted aligned reads. - -
- -[SAMTOOLS SORT](http://www.htslib.org/doc/samtools-sort.html) sort the aligned reads and convert the sam file in bam file. - ### TAMA COLLAPSE
Output files -- `08_GSTAMA_COLLAPSE/` +- `07_GSTAMA_COLLAPSE/` - `.chunk_collapsed.bed`: This is a bed12 format file containing the final collapsed version of your transcriptome - `.chunk_local_density_error.txt`: This file contains the log of filtering for local density error around the splice junctions - `.chunk_polya.txt`: This file contains the reads with potential poly A truncation @@ -175,8 +150,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
Output files -- `09_GSTAMA_FILELIST/` +- `08_GSTAMA_FILELIST/` - `.tsv`: A tsv listing bed files to merge with TAMA merge + - `all_samples.tsv`: A tsv listing bed files from all samples to merge with TAMA merge
@@ -187,7 +163,7 @@ TAMA FILELIST is a home script for generating input file list for TAMA merge.
Output files -- `10_GSTAMA_MERGE/` +- `09_GSTAMA_MERGE/` - `.bed`: This is the main merged annotation file. - `_gene_report.txt`: This contains a report of the genes from the merged file. - `_merge.txt`: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. @@ -195,7 +171,7 @@ TAMA FILELIST is a home script for generating input file list for TAMA merge.
-[TAMA MERGE](https://github.com/GenomeRIK/tama/wiki/Tama-Merge) TAMA Merge is a tool that allows you to merge multiple transcriptomes while maintaining source information. +[TAMA MERGE](https://github.com/GenomeRIK/tama/wiki/Tama-Merge) TAMA Merge is a tool that allows you to merge multiple transcriptomes while maintaining source information. When there are two or more samples, output files corresponding to `all_samples` are also stored if `--tama_merge_all` parameter is set. ### MultiQC @@ -226,4 +202,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/docs/usage.md b/docs/usage.md index 6b92974..0df9083 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -9,9 +9,15 @@ This pipeline has been designed to analyse several samples or sequencing runs at the same time. It reads all samples from a samplesheet file and parallelizes computation for each of them. -Depending on your on data, you might not need to run the isoseq preprocessing. -This step can be skipped by setting the `--entrypoint` parameter to `map` and starting the analysis from the mapping step. -By default, the entrypoint is set to `isoseq` and the full pipeline is run. +Depending on your data, you might not need to run the full Iso-Seq preprocessing. +Every row of the samplesheet carries a `start_from` value declaring where that sample +enters the pipeline, so a single run can mix raw subreads with data that has already +been through CCS, LIMA or refine: + +- `ccs` — raw subreads; runs the full pipeline (CCS, LIMA, refine, mapping) +- `lima` — CCS consensuses; skips CCS generation +- `refine` — Full Length reads produced by LIMA; skips CCS and LIMA +- `mapping` — long reads in FASTA; skips Iso-Seq preprocessing entirely ### Samplesheet input @@ -24,32 +30,47 @@ Use `--input` parameter to specify its location. The samplesheet is a comma-separated file with 4 columns, and a header row as shown in the examples below. -| Column | Description | -| -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. Spaces in sample names are automatically converted to underscores (`_`). | -| `bam` | Full path to isoseq subreads in `bam` format. | -| `pbi` | Full path to Pacbio index generated with [pbindex](https://github.com/pacificbiosciences/pbbam/). File's name must be compose of bam file name with the `.pbi` extension. | -| `reads` | Set of long reads to analyse in fasta format. The file must be gziped (.fa.gz). | +| Column | Description | +| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Sample name. Spaces in sample names are automatically converted to underscores (`_`). | +| `seq_data` | The path to the sequence file. A BAM file for subreads, Consensus Circular Sequences or Full Length sequences. A fasta file for long reads. | +| `pbi` | In case `seq_data` is a subreads BAM, the path to Pacbio index generated with [pbindex](https://github.com/pacificbiosciences/pbbam/). File's name must be composed of the bam file name with the `.pbi` extension. In the other cases, `none` | +| `start_from` | The value depends on the seq_data file. `ccs` for subreads, `lima` for ccs sequences, `refine` for Full Length data and `mapping` for long reads. | + +```csv +sample,seq_data,pbi,start_from +sample1,sample1.subreads.bam,sample1.subreads.bam.pbi,ccs +sample2,sample2.ccs.bam,none,lima +sample3,sample3.fl.primer_5p--primer_3p.bam,none,refine +sample4,sample4.long_reads.fa.gz,none,mapping +``` -Starting from `pbccs` (`isoseq` entrypoint), the columns `sample`, `bam`, `pbi` are mandatory. -The `reads` column must be set to `None`. +If multiple cells have been run for the same sample, the sample ID can be used several times in the samplesheet. Each dataset will be analysed in parallel and then merged with TAMA. -```console -sample,bam,pbi,reads -sample1,sample1.subreads.bam,sample1.subreads.bam.pbi,None -sample2,sample2.subreads.bam,sample2.subreads.bam.pbi,None +```csv +sample,seq_data,pbi,start_from +sample1,sample1_cell1.subreads.bam,sample1_cell1.subreads.bam.pbi,ccs +sample1,sample1_cell2.subreads.bam,sample1_cell2.subreads.bam.pbi,ccs +sample2,sample1.subreads.bam,sample2.subreads.bam.pbi,ccs ``` -If the `map` entrypoint is used, the `reads` column must be filled with a gzipped fasta file with long reads and `sample` must be set. -The `bam` and `pbi` columns have to be set to `None`. +Some example samplesheets can be found on the [github repository](https://github.com/nf-core/isoseq/tree/master/assets). -```console -sample,bam,pbi,reads -sample1,None,None,sample1.fa.gz -sample2,None,None,sample2.fa.gz -``` +### Migrating from version 2.0.0 -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +Version 3.0.0 redefines the samplesheet, so samplesheets written for 2.0.0 will not validate. + +| Version 2.0.0 | Version 3.0.0 | +| ------------------------------------------- | --------------------------------------- | +| `sample,bam,pbi,reads` | `sample,seq_data,pbi,start_from` | +| separate `bam` and `reads` columns | one `seq_data` column holding either | +| `None` placeholder | `none`, lower case, for an absent `pbi` | +| `--entrypoint isoseq` or `--entrypoint map` | a `start_from` value on every row | + +Two parameter changes also affect existing command lines: + +- `--chunk` has been split into `--chunk_ccs` and `--chunk_mapping`, controlling chunking of CCS generation and of mapping independently. +- `--max_cpus`, `--max_memory` and `--max_time` have been removed by the nf-core template. Set limits with the `resourceLimits` directive in a custom config instead. ### Primer file @@ -70,6 +91,10 @@ Use the --primers option to specify its location. --primers '[path to primers file]' ``` +The primer file is only used by `LIMA` and `isoseq refine`, so it is required whenever at +least one samplesheet row uses `start_from` `ccs`, `lima` or `refine`. If every row uses +`mapping`, neither step runs and `--primers` can be omitted. + ### Reference genome and annotation The reference genome sequence is mandatory and must be in `FASTA` format. @@ -88,14 +113,6 @@ Two aligners are available. The `uLTRA` aligner helps to detect small exons with --aligner '[ultra,minimap2]' ``` -### Entrypoint - -The mapping and the alignment analysis are agnostic to the kind long reads used. If your sequencing company provides pre-computed HiFi reads or you want to use nanopore sequences, you can skip the isoseq preprocessing and start the analysis from the mapping step. - -```console ---entrypoint 'map' -``` - ## Running the pipeline The typical command for running the pipeline is as follows: @@ -119,9 +136,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -129,9 +145,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/isoseq -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -150,23 +166,21 @@ nextflow pull nf-core/isoseq ### Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [nf-core/isoseq releases page](https://github.com/nf-core/isoseq/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -174,16 +188,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -197,11 +210,11 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `shifter` - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) + - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. @@ -219,21 +232,21 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs @@ -243,14 +256,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf old mode 100644 new mode 100755 index 92e8963..a32c602 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GENOME PARAMETER VALUES @@ -53,12 +51,14 @@ workflow NFCORE_ISOSEQ { // WORKFLOW: Run pipeline // ISOSEQ ( - samplesheet + samplesheet, + params.multiqc_config, + params.multiqc_logo, + params.multiqc_methods_description, + params.outdir, ) - emit: multiqc_report = ISOSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,20 +69,22 @@ workflow NFCORE_ISOSEQ { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.help, + params.help_full, + params.show_hidden ) + // // WORKFLOW: Run main workflow // @@ -99,7 +101,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_ISOSEQ.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 8d4d526..cbd5ced 100644 --- a/modules.json +++ b/modules.json @@ -7,72 +7,67 @@ "nf-core": { "bamtools/convert": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] - }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "gnu/sort": { "branch": "master", - "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "gstama/collapse": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "ecace0debef350b6636ea603824ae16c1bb29a54", "installed_by": ["modules"] }, "gstama/merge": { "branch": "master", - "git_sha": "3528e946c9f19501d78cf0901d0b57e13e2f6860", + "git_sha": "ecace0debef350b6636ea603824ae16c1bb29a54", "installed_by": ["modules"] }, "gstama/polyacleanup": { "branch": "master", - "git_sha": "8684e27e1061f855822ecc77d5099bc08f858784", + "git_sha": "82450e2e06bc03df52e8adbe8886de25adb402ee", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c", "installed_by": ["modules"] }, "isoseq/refine": { "branch": "master", - "git_sha": "8da47884cbd6c7a8d849f8cf53340511ab00df51", + "git_sha": "17bf175c37d61ae3ba8b1e0bd972f3f880327497", "installed_by": ["modules"] }, "lima": { "branch": "master", - "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "minimap2/align": { "branch": "master", - "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306", + "git_sha": "135d883a43b1a2324b4112cd270cf22e20835533", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "fe9614c5d1d9820dae56a5e30a07ba336db45835", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] }, "pbccs": { "branch": "master", - "git_sha": "8da47884cbd6c7a8d849f8cf53340511ab00df51", + "git_sha": "14fc45a90d03d4820e3f08fce68970b4499bba22", "installed_by": ["modules"] }, "ultra/align": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "69993a757b03f6fbc50b06b226c00b5083543574", "installed_by": ["modules"] }, "ultra/index": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "69993a757b03f6fbc50b06b226c00b5083543574", "installed_by": ["modules"] } } @@ -81,17 +76,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436", "installed_by": ["subworkflows"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 787fe1b..0000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/isoseq/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/bamtools/convert/environment.yml b/modules/nf-core/bamtools/convert/environment.yml index 1407c34..5ee3360 100644 --- a/modules/nf-core/bamtools/convert/environment.yml +++ b/modules/nf-core/bamtools/convert/environment.yml @@ -1,7 +1,7 @@ -name: bamtools_convert +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamtools=2.5.2 diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf index 71c3774..2fee0b7 100644 --- a/modules/nf-core/bamtools/convert/main.nf +++ b/modules/nf-core/bamtools/convert/main.nf @@ -3,38 +3,44 @@ process BAMTOOLS_CONVERT { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hdcf5f25_2' : - 'biocontainers/bamtools:2.5.2--hdcf5f25_2' }" + 'quay.io/biocontainers/bamtools:2.5.2--hdcf5f25_2' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bamtools'), eval("bamtools --version | sed '2!d;s/bamtools //g'"), emit: versions_bamtools, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/ - if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml" - m = args =~ /-format ([a-z]+)/ - ext = m[0][1] + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + format_cmd = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/ + matched_format = args =~ /-format ([a-z]+)/ + extension = matched_format[0][1] + if ( format_cmd == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml" """ bamtools \\ convert \\ $args \\ -in $bam \\ - -out ${prefix}.${ext} + -out ${prefix}.${extension} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + format_cmd = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/ + matched_format = args =~ /-format ([a-z]+)/ + extension = matched_format[0][1] + if ( format_cmd == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml" - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' ) - END_VERSIONS + """ + touch ${prefix}.${extension} """ } diff --git a/modules/nf-core/bamtools/convert/meta.yml b/modules/nf-core/bamtools/convert/meta.yml index 3cc8ae6..992f0ef 100644 --- a/modules/nf-core/bamtools/convert/meta.yml +++ b/modules/nf-core/bamtools/convert/meta.yml @@ -1,5 +1,6 @@ name: bamtools_convert -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - bamtools/convert @@ -19,31 +20,55 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - out: - type: file - description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml) - pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bed,fasta,fastq,json,pileup,sam,yaml}": + type: file + description: Output file + pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_3464 # JSON + - edam: http://edamontology.org/format_3750 # YAML + versions_bamtools: + - - "${task.process}": + type: string + description: The name of the process + - bamtools: + type: string + description: The name of the tool + - "bamtools --version | sed '2!d;s/bamtools //g'": + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: - "@sguizard" +topics: + versions: + - - "${task.process}": + type: string + description: The name of the process + - bamtools: + type: string + description: The name of the tool + - "bamtools --version | sed '2!d;s/bamtools //g'": + type: eval + description: The expression to obtain the version of the tool diff --git a/modules/nf-core/bamtools/convert/tests/main.nf.test b/modules/nf-core/bamtools/convert/tests/main.nf.test new file mode 100644 index 0000000..385288e --- /dev/null +++ b/modules/nf-core/bamtools/convert/tests/main.nf.test @@ -0,0 +1,233 @@ +nextflow_process { + + name "Test Process BAMTOOLS_CONVERT" + config "./nextflow.config" + script "../main.nf" + process "BAMTOOLS_CONVERT" + + tag "modules" + tag "modules_nfcore" + tag "bamtools" + tag "bamtools/convert" + + test("test_bamtools_convert_ext_error") { + when { + params { + module_args = "-format vcf" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.failed }, + { assert process.errorReport.contains("-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml") } + ) + } + } + test("test_bamtools_convert_noext_error") { + when { + params { + module_args = "" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.failed }, + { assert process.errorReport.contains("-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml") } + ) + } + } + test("test_bamtools_convert_bed") { + when { + params { + module_args = "-format bed" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_fasta") { + when { + params { + module_args = "-format fasta" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_fastq") { + when { + params { + module_args = "-format fastq" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_json") { + + + when { + params { + module_args = "-format json" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_pileup") { + + + when { + params { + module_args = "-format pileup" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_sam") { + + + when { + params { + module_args = "-format sam" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_bamtools_convert_yaml") { + when { + params { + module_args = "-format yaml" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_bamtools_convert_yaml - stub") { + when { + params { + module_args = "-format yaml" + } + process { + """ + input[0] = [ + [id:'test', single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + process.out.versions.collect{path(it).yaml} + ).match() } + ) + } + } +} diff --git a/modules/nf-core/bamtools/convert/tests/main.nf.test.snap b/modules/nf-core/bamtools/convert/tests/main.nf.test.snap new file mode 100644 index 0000000..23f8062 --- /dev/null +++ b/modules/nf-core/bamtools/convert/tests/main.nf.test.snap @@ -0,0 +1,349 @@ +{ + "test_bamtools_convert_bed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,4e34cc15bf31e700f5f3a9f8fffb6c81" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,4e34cc15bf31e700f5f3a9f8fffb6c81" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:52:31.973880179", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_pileup": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pileup:md5,e5a3cb4a3e1bf980a575fafce6a2826f" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pileup:md5,e5a3cb4a3e1bf980a575fafce6a2826f" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:53:23.017380988", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_yaml": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.yaml:md5,68b56f198da036fef33e150eb773dc3b" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.yaml:md5,68b56f198da036fef33e150eb773dc3b" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:53:50.989109105", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_yaml - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.yaml:md5,68b56f198da036fef33e150eb773dc3b" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.yaml:md5,68b56f198da036fef33e150eb773dc3b" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + }, + [ + + ] + ], + "timestamp": "2026-03-11T18:54:05.904431089", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,52aeacf78571862b7e97c7d44ac8f827" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,52aeacf78571862b7e97c7d44ac8f827" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:52:44.670839319", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastq:md5,e591c48daad2c56638e5d6f21f1f71c5" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastq:md5,e591c48daad2c56638e5d6f21f1f71c5" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:52:56.91010697", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_json": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.json:md5,9c44279e6da864f30b52a79a14dcb2bd" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.json:md5,9c44279e6da864f30b52a79a14dcb2bd" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:53:09.39949925", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test_bamtools_convert_sam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sam:md5,6f559e53e1ea7ff3dc919c8c4695de96" + ] + ], + "1": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ], + "data": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sam:md5,6f559e53e1ea7ff3dc919c8c4695de96" + ] + ], + "versions_bamtools": [ + [ + "BAMTOOLS_CONVERT", + "bamtools", + "2.5.2" + ] + ] + } + ], + "timestamp": "2026-03-11T18:53:35.676586302", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/bamtools/convert/tests/nextflow.config b/modules/nf-core/bamtools/convert/tests/nextflow.config new file mode 100644 index 0000000..aff333e --- /dev/null +++ b/modules/nf-core/bamtools/convert/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: "BAMTOOLS_CONVERT" { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index b48ced2..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.20 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index 105f926..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5f..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100644 index 9a493ac..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,100 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - -import yaml -import platform -from textwrap import dedent - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
Process Name Software Version
{process if (i == 0) else ''}{tool}{version}
") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a93..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml deleted file mode 100644 index 1787b38..0000000 --- a/modules/nf-core/fastqc/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: fastqc -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 70edae4..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert path(process.out.html[0][1][2]).text.contains("") }, - { assert path(process.out.html[0][1][3]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } - ) - } - } - -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index 86f7c31..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "fastqc_versions_interleaved": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:07.293713" - }, - "fastqc_stub": { - "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:31:01.425198" - }, - "fastqc_versions_multiple": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:55.797907" - }, - "fastqc_versions_bam": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:26.795862" - }, - "fastqc_versions_single": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:27.043675" - }, - "fastqc_versions_paired": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:47.584191" - }, - "fastqc_versions_custom_prefix": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:41:14.576531" - } -} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294..0000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/gnu/sort/environment.yml b/modules/nf-core/gnu/sort/environment.yml index eb9b77e..0c4cd94 100644 --- a/modules/nf-core/gnu/sort/environment.yml +++ b/modules/nf-core/gnu/sort/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: gnu_sort channels: - conda-forge - bioconda - - defaults dependencies: - - conda-forge::coreutils=9.3 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/gnu/sort/main.nf b/modules/nf-core/gnu/sort/main.nf index e116766..142ef14 100644 --- a/modules/nf-core/gnu/sort/main.nf +++ b/modules/nf-core/gnu/sort/main.nf @@ -3,16 +3,16 @@ process GNU_SORT { label "process_low" conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/coreutils:9.3': - 'biocontainers/coreutils:9.3' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/coreutils:9.5': + 'quay.io/biocontainers/coreutils:9.5' }" input: - tuple val(meta), path(input) + tuple val(meta), path(input), val(suffix) output: - tuple val(meta), file( "${output_file}" ) , emit: sorted - path "versions.yml" , emit: versions + tuple val(meta), path( "${output_file}" ) , emit: sorted + tuple val("${task.process}"), val('coreutils'), eval("sort --version |& sed '1!d ; s/sort (GNU coreutils) //'"), emit: versions_coreutils, topic: versions when: task.ext.when == null || task.ext.when @@ -20,32 +20,17 @@ process GNU_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.extension}" output_file = "${prefix}.${suffix}" - def VERSION = "9.3" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ sort ${args} ${input} > ${output_file} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.extension}" output_file = "${prefix}.${suffix}" - def VERSION = "9.3" - if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${output_file} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml index 9d96175..0f07bde 100644 --- a/modules/nf-core/gnu/sort/meta.yml +++ b/modules/nf-core/gnu/sort/meta.yml @@ -3,38 +3,69 @@ description: | Writes a sorted concatenation of file/s keywords: - GNU + - coreutils - sort - merge compare tools: - - sort: - description: "Writes a sorted concatenation of file/s" - homepage: "https://github.com/vgl-hub/gfastats" - documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html" + - gnu: + description: "The GNU Core Utilities are the basic file, shell and text manipulation + utilities of the GNU operating system. These are the core utilities which are + expected to exist on every operating system." + homepage: "https://www.gnu.org/software/coreutils/" + documentation: "https://www.gnu.org/software/coreutils/manual/html_node/index.html" + tool_dev_url: "https://git.savannah.gnu.org/cgit/coreutils.git" + doi: "10.5281/zenodo.581670" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Draft assembly file - pattern: "*.{txt,bed,interval,genome,bins}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Draft assembly file + pattern: "*.{txt,bed,interval,genome,bins}" + ontologies: [] + - suffix: + type: string + description: Output suffix output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sorted: - type: file - description: The sorted txt file generated by sort - pattern: "*.{txt,bed,interval,genome,bins}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + sorted: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "${output_file}" + - "${output_file}": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "${output_file}" + versions_coreutils: + - - ${task.process}: + type: string + description: The process the versions were collected from + - coreutils: + type: string + description: The tool name + - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - coreutils: + type: string + description: The tool name + - "sort --version |& sed '1!d ; s/sort (GNU coreutils) //'": + type: string + description: The command used to generate the version of the tool authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test b/modules/nf-core/gnu/sort/tests/main.nf.test index e403018..738a1f9 100644 --- a/modules/nf-core/gnu/sort/tests/main.nf.test +++ b/modules/nf-core/gnu/sort/tests/main.nf.test @@ -10,16 +10,18 @@ nextflow_process { tag "gnu/sort" test("unsorted_genome_sort") { - config "./sort_simple_bed.config" when { + params { + gnu_sort_args = "-k1,1 -k2,2n" + } process { """ input[0] = [ - [id:'genome_test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['genome_file'], - checkIfExists: true) - ] + [id:'genome_test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.genome', checkIfExists: true), + "genome.sorted" + ] """ } } @@ -27,26 +29,25 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.sorted[0][1]).name - ).match("genome_sort") - } + { assert snapshot(process.out).match() } ) } } test("unsorted_intervals_sort") { - config "./sort_simple_bed.config" + when { + params { + gnu_sort_args = "-k1,1 -k2,2n" + } process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['intervals'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.bed', checkIfExists: true), + "bed.sorted" + ] """ } } @@ -54,27 +55,25 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.sorted[0][1]).name - ).match("interval_sort") - } + { assert snapshot(process.out).match() } ) } } test("unsorted_csv_sort") { - config "./sort_complex.config" when { + params { + gnu_sort_args = "-t ';' -g -k 1,1 -k 2,2" + } process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true), + "csv.sorted" + ] """ } } @@ -82,28 +81,27 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.sorted[0][1]).name - ).match("csv_sort") - } + { assert snapshot(process.out).match() } ) } } test("unsorted_csv_sort_stub") { - config "./sort_complex.config" + options "-stub" when { + params { + gnu_sort_args = "-t ';' -g -k 1,1 -k 2,2" + } process { """ input[0] = [ - [id:'test'], - file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], - checkIfExists: true) - ] + [id:'test'], + file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true), + "csv.sorted" + ] """ } } @@ -111,7 +109,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test.snap b/modules/nf-core/gnu/sort/tests/main.nf.test.snap index 63891bc..1929dd2 100644 --- a/modules/nf-core/gnu/sort/tests/main.nf.test.snap +++ b/modules/nf-core/gnu/sort/tests/main.nf.test.snap @@ -7,40 +7,38 @@ { "id": "test" }, - "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + "test.csv.sorted:md5,797450743dae151378fa5b7a9b5f38cc" ] ], "1": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ], "sorted": [ [ { "id": "test" }, - "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + "test.csv.sorted:md5,797450743dae151378fa5b7a9b5f38cc" ] ], - "versions": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + "versions_coreutils": [ + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-14T11:13:44.714632791" - }, - "interval_sort": { - "content": [ - "test.bed.sorted" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.10.4" }, - "timestamp": "2024-06-14T11:13:37.962807086" + "timestamp": "2026-03-27T16:25:51.135939" }, "unsorted_csv_sort_stub": { "content": [ @@ -54,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ], "sorted": [ [ @@ -64,26 +66,20 @@ "test.csv.sorted:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + "versions_coreutils": [ + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2024-06-14T11:13:51.456258705" - }, - "csv_sort": { - "content": [ - "test.csv.sorted" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-14T11:13:44.725431761" + "timestamp": "2026-01-23T15:48:45.534463019" }, "unsorted_genome_sort": { "content": [ @@ -93,40 +89,38 @@ { "id": "genome_test" }, - "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + "genome_test.genome.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" ] ], "1": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ], "sorted": [ [ { "id": "genome_test" }, - "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + "genome_test.genome.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" ] ], - "versions": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + "versions_coreutils": [ + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.10.4" }, - "timestamp": "2024-06-14T11:13:31.041778719" - }, - "genome_sort": { - "content": [ - "genome_test.bed.sorted" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-14T11:13:31.060201722" + "timestamp": "2026-03-27T16:25:43.198666" }, "unsorted_intervals_sort": { "content": [ @@ -140,7 +134,11 @@ ] ], "1": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ], "sorted": [ [ @@ -150,15 +148,19 @@ "test.bed.sorted:md5,abbce903ef263d38b2f71856387799ab" ] ], - "versions": [ - "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + "versions_coreutils": [ + [ + "GNU_SORT", + "coreutils", + "9.5" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2024-06-14T11:13:37.951397547" + "timestamp": "2026-01-23T15:48:11.626509684" } } \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/nextflow.config b/modules/nf-core/gnu/sort/tests/nextflow.config new file mode 100644 index 0000000..2d6d3ed --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GNU_SORT { + ext.args = params.gnu_sort_args + } +} diff --git a/modules/nf-core/gnu/sort/tests/sort_complex.config b/modules/nf-core/gnu/sort/tests/sort_complex.config deleted file mode 100644 index 103eaaf..0000000 --- a/modules/nf-core/gnu/sort/tests/sort_complex.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: GNU_SORT { - ext.args = { "-t ';' -g -k 1,1 -k 2,2" } - ext.suffix = { "csv.sorted" } - } -} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_bed.config b/modules/nf-core/gnu/sort/tests/sort_simple_bed.config deleted file mode 100644 index d7d52e0..0000000 --- a/modules/nf-core/gnu/sort/tests/sort_simple_bed.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: GNU_SORT { - ext.args = { "-k1,1 -k2,2n" } - ext.suffix = { "bed.sorted" } - } -} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_genome.config b/modules/nf-core/gnu/sort/tests/sort_simple_genome.config deleted file mode 100644 index 4dcec38..0000000 --- a/modules/nf-core/gnu/sort/tests/sort_simple_genome.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: GNU_SORT { - ext.args = { "-k1,1 -k2,2n" } - ext.suffix = { "genome.sorted" } - } -} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/tags.yml b/modules/nf-core/gnu/sort/tests/tags.yml deleted file mode 100644 index ac40e37..0000000 --- a/modules/nf-core/gnu/sort/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gnu/sort: - - "modules/nf-core/gnu/sort/**" diff --git a/modules/nf-core/gstama/collapse/environment.yml b/modules/nf-core/gstama/collapse/environment.yml index 644bc6c..46813d0 100644 --- a/modules/nf-core/gstama/collapse/environment.yml +++ b/modules/nf-core/gstama/collapse/environment.yml @@ -1,7 +1,7 @@ -name: GSTAMA_COLLAPSE +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gstama/collapse/main.nf b/modules/nf-core/gstama/collapse/main.nf index ec3f955..a3e5592 100644 --- a/modules/nf-core/gstama/collapse/main.nf +++ b/modules/nf-core/gstama/collapse/main.nf @@ -3,9 +3,9 @@ process GSTAMA_COLLAPSE { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : - 'biocontainers/gs-tama:1.0.3--hdfd78af_0' }" + 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" input: tuple val(meta), path(bam) @@ -19,10 +19,9 @@ process GSTAMA_COLLAPSE { tuple val(meta), path("*_read.txt") , emit: read tuple val(meta), path("*_strand_check.txt") , emit: strand_check tuple val(meta), path("*_trans_report.txt") , emit: trans_report - path "versions.yml" , emit: versions - tuple val(meta), path("*_varcov.txt") , emit: varcov , optional: true tuple val(meta), path("*_variants.txt") , emit: variants, optional: true + tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions when: task.ext.when == null || task.ext.when @@ -32,14 +31,18 @@ process GSTAMA_COLLAPSE { def prefix = task.ext.prefix ?: "${meta.id}" """ tama_collapse.py \\ - -s $bam \\ - -f $fasta \\ + -s ${bam} \\ + -f ${fasta} \\ -p ${prefix} \\ - $args + ${args} + """ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' ) - END_VERSIONS + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}_{collapsed,trans_read}.bed + touch ${prefix}_{local_density_error,polya,read}.txt + touch ${prefix}_{strand_check,trans_report,varcov,variants}.txt """ } diff --git a/modules/nf-core/gstama/collapse/meta.yml b/modules/nf-core/gstama/collapse/meta.yml index 209ba75..ce21b6c 100644 --- a/modules/nf-core/gstama/collapse/meta.yml +++ b/modules/nf-core/gstama/collapse/meta.yml @@ -1,4 +1,4 @@ -name: GSTAMA_COLLAPSE +name: gstama_collapse description: Collapse redundant transcript models in Iso-Seq data. keywords: - tama_collapse.py @@ -15,67 +15,166 @@ tools: documentation: https://github.com/GenomeRIK/tama/wiki tool_dev_url: https://github.com/sguizard/gs-tama doi: 10.1186/s12864-020-07123-7 - licence: GNU GPL3 + licence: + - "GNU GPL3" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A sorted BAM or sam file of aligned reads - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: A sorted BAM or sam file of aligned reads + pattern: "*.{bam,sam}" + ontologies: [] - fasta: type: file description: A fasta file of the genome used for the mapping pattern: "*.{fasta,fa}" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bed: - type: file - description: a bed12 format file containing the final collapsed version of your transcriptome - pattern: "*.bed" - - bed_trans_reads: - type: file - description: This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models. - pattern: "*_trans_read.bed" - - local_density_error: - type: file - description: This file contains the log of filtering for local density error around the splice junctions ("-lde") - pattern: "*_local_density_error.txt" - - polya: - type: file - description: This file contains the reads with potential poly A truncation. - pattern: "*_polya.txt" - - read: - type: file - description: This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file - pattern: "*_read.txt" - - strand_check: - type: file - description: This file shows instances where the sam flag strand information contrasted the GMAP strand information. - pattern: "*_strand_check.txt" - - trans_report: - type: file - description: This file contains collapsing information for each transcript. - pattern: "*_trans_report.txt" - - varcov: - type: file - description: This file contains the coverage information for each variant detected. - pattern: "*_varcov.txt" - - variants: - type: file - description: This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo. - pattern: "*_variants.txt" + bed: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_collapsed.bed": + type: file + description: a bed12 format file containing the final collapsed version + of your transcriptome + pattern: "*.bed" + ontologies: [] + bed_trans_reads: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_read.bed": + type: file + description: This file uses bed12 format to show the transcript model + for each read based on the mapping prior to collapsing. This only + contains the reads which were accepted according to the defined + thresholds. You can use this file to see if there were any strange + occurrences during collapsing. It also contains the relationships + between reads and collapsed transcript models. The 1st subfield in the + 4th column shows the final transcript ID and the 2nd subfield in the + 4th column shows the read ID. If you used no_cap mode for collapsing + there may be multiple lines for a single read. This happens when a 5' + degraded read can match to multiple 5' longer transcript models. + pattern: "*_trans_read.bed" + ontologies: [] + local_density_error: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_local_density_error.txt": + type: file + description: This file contains the log of filtering for local density + error around the splice junctions ("-lde") + pattern: "*_local_density_error.txt" + ontologies: [] + polya: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_polya.txt": + type: file + description: This file contains the reads with potential poly A + truncation. + pattern: "*_polya.txt" + ontologies: [] + read: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_read.txt": + type: file + description: This file contains information for all mapped reads from + the input SAM/BAM file. It shows both accepted and discarded reads and + should match the number of mapped reads in your SAM/BAM file + pattern: "*_read.txt" + ontologies: [] + strand_check: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_strand_check.txt": + type: file + description: This file shows instances where the sam flag strand + information contrasted the GMAP strand information. + pattern: "*_strand_check.txt" + ontologies: [] + trans_report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This file contains collapsing information for each + transcript. + pattern: "*_trans_report.txt" + ontologies: [] + varcov: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_varcov.txt": + type: file + description: This file contains the coverage information for each + variant detected. + pattern: "*_varcov.txt" + ontologies: [] + variants: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_variants.txt": + type: file + description: This file contains the variants called. Variants are only + called if 5 or more reads show the variant at a specific locus. If you + would like to change the threshold, please make an issue about this in + the Github repo. + pattern: "*_variants.txt" + ontologies: [] + versions_gstama: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_collapse.py -version | sed -n 's/tc_version_date_//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_collapse.py -version | sed -n 's/tc_version_date_//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/collapse/tests/main.nf.test b/modules/nf-core/gstama/collapse/tests/main.nf.test new file mode 100644 index 0000000..9adc6fd --- /dev/null +++ b/modules/nf-core/gstama/collapse/tests/main.nf.test @@ -0,0 +1,58 @@ + +nextflow_process { + + name "Test Process GSTAMA_COLLAPSE" + script "../main.nf" + process "GSTAMA_COLLAPSE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/collapse" + + test("test-gstama-collapse") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-gstama-collapse -- stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + +} diff --git a/modules/nf-core/gstama/collapse/tests/main.nf.test.snap b/modules/nf-core/gstama/collapse/tests/main.nf.test.snap new file mode 100644 index 0000000..53773b2 --- /dev/null +++ b/modules/nf-core/gstama/collapse/tests/main.nf.test.snap @@ -0,0 +1,182 @@ +{ + "test-gstama-collapse -- stub": { + "content": [ + { + "bed": [ + [ + { + "id": "test" + }, + "test_tc_collapsed.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bed_trans_reads": [ + [ + { + "id": "test" + }, + "test_tc_trans_read.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "local_density_error": [ + [ + { + "id": "test" + }, + "test_tc_local_density_error.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "polya": [ + [ + { + "id": "test" + }, + "test_tc_polya.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "read": [ + [ + { + "id": "test" + }, + "test_tc_read.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "strand_check": [ + [ + { + "id": "test" + }, + "test_tc_strand_check.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "trans_report": [ + [ + { + "id": "test" + }, + "test_tc_trans_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "varcov": [ + [ + { + "id": "test" + }, + "test_tc_varcov.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "variants": [ + [ + { + "id": "test" + }, + "test_tc_variants.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_COLLAPSE", + "gstama", + "2021_11_03" + ] + ] + } + ], + "timestamp": "2026-05-11T22:55:53.631912293", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.03.2" + } + }, + "test-gstama-collapse": { + "content": [ + { + "bed": [ + [ + { + "id": "test" + }, + "test_tc_collapsed.bed:md5,e5105198ed970a33ae0ecaa7bff421d9" + ] + ], + "bed_trans_reads": [ + [ + { + "id": "test" + }, + "test_tc_trans_read.bed:md5,0ca1a32f33ef05242d897d913802554b" + ] + ], + "local_density_error": [ + [ + { + "id": "test" + }, + "test_tc_local_density_error.txt:md5,b917ac1f14eccd590b6881a686f324d5" + ] + ], + "polya": [ + [ + { + "id": "test" + }, + "test_tc_polya.txt:md5,628ea62b918fc4f31e109f724d714a66" + ] + ], + "read": [ + [ + { + "id": "test" + }, + "test_tc_read.txt:md5,d2685d7f24cd1611e0770a5ce25422fe" + ] + ], + "strand_check": [ + [ + { + "id": "test" + }, + "test_tc_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec" + ] + ], + "trans_report": [ + [ + { + "id": "test" + }, + "test_tc_trans_report.txt:md5,33a86c15ca2acce36b2a5962f4c1adc4" + ] + ], + "varcov": [ + [ + { + "id": "test" + }, + "test_tc_varcov.txt:md5,587fd899ff658eb66b1770a35283bfcb" + ] + ], + "variants": [ + [ + { + "id": "test" + }, + "test_tc_variants.txt:md5,5b1165e9f33faba4f7207013fc27257e" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_COLLAPSE", + "gstama", + "2021_11_03" + ] + ] + } + ], + "timestamp": "2026-05-11T22:57:16.945475905", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.03.2" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gstama/collapse/tests/nextflow.config b/modules/nf-core/gstama/collapse/tests/nextflow.config new file mode 100644 index 0000000..ea89a16 --- /dev/null +++ b/modules/nf-core/gstama/collapse/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GSTAMA_COLLAPSE { + ext.args = '-x capped -b BAM' + ext.prefix = { "${meta.id}_tc" } + } +} diff --git a/modules/nf-core/gstama/merge/environment.yml b/modules/nf-core/gstama/merge/environment.yml index 44d5741..46813d0 100644 --- a/modules/nf-core/gstama/merge/environment.yml +++ b/modules/nf-core/gstama/merge/environment.yml @@ -1,7 +1,7 @@ -name: gstama_merge +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gstama/merge/main.nf b/modules/nf-core/gstama/merge/main.nf index 8b67c47..563e2ce 100644 --- a/modules/nf-core/gstama/merge/main.nf +++ b/modules/nf-core/gstama/merge/main.nf @@ -3,9 +3,9 @@ process GSTAMA_MERGE { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : - 'biocontainers/gs-tama:1.0.3--hdfd78af_0' }" + 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" input: tuple val(meta), path(bed) @@ -16,7 +16,7 @@ process GSTAMA_MERGE { tuple val(meta), path("*_gene_report.txt") , emit: gene_report tuple val(meta), path("*_merge.txt") , emit: merge tuple val(meta), path("*_trans_report.txt"), emit: trans_report - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gstama'), eval("tama_merge.py -version | sed '1!d'"), emit: versions_gstama, topic: versions when: task.ext.when == null || task.ext.when @@ -26,14 +26,16 @@ process GSTAMA_MERGE { def prefix = task.ext.prefix ?: "${meta.id}" """ tama_merge.py \\ - -f $filelist \\ + -f ${filelist} \\ -d merge_dup \\ -p ${prefix} \\ - $args + ${args} + """ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gstama: \$( tama_merge.py -version | head -n1 ) - END_VERSIONS + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + touch ${prefix}_{gene_report,merge,trans_report}.txt """ } diff --git a/modules/nf-core/gstama/merge/meta.yml b/modules/nf-core/gstama/merge/meta.yml index adb2b32..694ad12 100644 --- a/modules/nf-core/gstama/merge/meta.yml +++ b/modules/nf-core/gstama/merge/meta.yml @@ -16,43 +16,106 @@ tools: documentation: https://github.com/GenomeRIK/tama/wiki tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" - licence: ["GPL v3 License"] + licence: + - "GPL v3 License" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed12 file generated by TAMA collapse + pattern: "*.bed" + ontologies: [] + - filelist: type: file - description: bed12 file generated by TAMA collapse - pattern: "*.bed" + description: list of files + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bed: - type: file - description: This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta. - pattern: "*.bed" - - gene_report: - type: file - description: This contains a report of the genes from the merged file. "num_clusters" refers to the number of source transcripts that were used to make this gene model. "num_final_trans" refers to the number of transcripts in the final gene model. - pattern: "*_gene_report.txt" - - merge: - type: file - description: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the "txt" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix. - pattern: "*_merge.txt" - - trans_report: - type: file - description: This contains the source information for each merged transcript. - pattern: "*_trans_report.txt" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + bed: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bed": + type: file + description: This is the main merged annotation file. Transcripts are + coloured according to the source support for each model. Sources are + numbered based on the order supplied in the input filelist file. For + example the first file named in the filelist file would have its + transcripts coloured in red. If a transcript has multiple sources the + colour is shown as magenta. + pattern: "*.bed" + ontologies: [] + gene_report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_gene_report.txt": + type: file + description: This contains a report of the genes from the merged file. + "num_clusters" refers to the number of source transcripts that were + used to make this gene model. "num_final_trans" refers to the number + of transcripts in the final gene model. + pattern: "*_gene_report.txt" + ontologies: [] + merge: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_merge.txt": + type: file + description: This contains a bed12 format file which shows the + coordinates of each input transcript matched to the merged transcript + ID. I used the "txt" extension even though it is a bed file just to + avoid confusion with the main bed file. You can use this file to map + the final merged transcript models to their pre-merged supporting + transcripts. The 1st subfield in the 4th column shows the final merged + transcript ID while the 2nd subfield shows the pre-merged transcript + ID with source prefix. + pattern: "*_merge.txt" + ontologies: [] + trans_report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This contains the source information for each merged + transcript. + pattern: "*_trans_report.txt" + ontologies: [] + versions_gstama: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_merge.py -version | sed '1!d': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_merge.py -version | sed '1!d': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test b/modules/nf-core/gstama/merge/tests/main.nf.test new file mode 100644 index 0000000..1741417 --- /dev/null +++ b/modules/nf-core/gstama/merge/tests/main.nf.test @@ -0,0 +1,63 @@ + +nextflow_process { + + name "Test Process GSTAMA_MERGE" + script "../main.nf" + process "GSTAMA_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/merge" + + test("test-gstama-merge") { + + when { + process { + """ + input[0] = [ + [ id:'test_all' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/txt/filelist.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-gstama-merge -- stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test_all' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/txt/filelist.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + +} diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test.snap b/modules/nf-core/gstama/merge/tests/main.nf.test.snap new file mode 100644 index 0000000..856f083 --- /dev/null +++ b/modules/nf-core/gstama/merge/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "test-gstama-merge -- stub": { + "content": [ + { + "bed": [ + [ + { + "id": "test_all" + }, + "test_all.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gene_report": [ + [ + { + "id": "test_all" + }, + "test_all_gene_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "merge": [ + [ + { + "id": "test_all" + }, + "test_all_merge.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "trans_report": [ + [ + { + "id": "test_all" + }, + "test_all_trans_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_MERGE", + "gstama", + "0.0.1" + ] + ] + } + ], + "timestamp": "2026-05-11T23:14:32.80541933", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.03.2" + } + }, + "test-gstama-merge": { + "content": [ + { + "bed": [ + [ + { + "id": "test_all" + }, + "test_all.bed:md5,60ec34e1ff9655d4ce2e83d3f4bbf448" + ] + ], + "gene_report": [ + [ + { + "id": "test_all" + }, + "test_all_gene_report.txt:md5,7029fd183dfd905a233403cfbe44722a" + ] + ], + "merge": [ + [ + { + "id": "test_all" + }, + "test_all_merge.txt:md5,4279e59ed5739ce4f2f811568962893f" + ] + ], + "trans_report": [ + [ + { + "id": "test_all" + }, + "test_all_trans_report.txt:md5,97d8346d9eb9da140941656c3a3325cd" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_MERGE", + "gstama", + "0.0.1" + ] + ] + } + ], + "timestamp": "2026-05-11T23:14:24.624282272", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.03.2" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gstama/polyacleanup/environment.yml b/modules/nf-core/gstama/polyacleanup/environment.yml index 7c143ff..46813d0 100644 --- a/modules/nf-core/gstama/polyacleanup/environment.yml +++ b/modules/nf-core/gstama/polyacleanup/environment.yml @@ -1,7 +1,7 @@ -name: gstama_polyacleanup +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gstama/polyacleanup/main.nf b/modules/nf-core/gstama/polyacleanup/main.nf index db2ed2b..525c573 100644 --- a/modules/nf-core/gstama/polyacleanup/main.nf +++ b/modules/nf-core/gstama/polyacleanup/main.nf @@ -3,38 +3,42 @@ process GSTAMA_POLYACLEANUP { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0': - 'biocontainers/gs-tama:1.0.3--hdfd78af_0' }" + 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" input: tuple val(meta), path(fasta) output: - tuple val(meta), path("*_tama.fa.gz") , emit: fasta - tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report - tuple val(meta), path("*_tama_tails.fa.gz") , emit: tails - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.fa.gz") , emit: fasta + tuple val(meta), path("${prefix}_polya_flnc_report.txt.gz"), emit: report + tuple val(meta), path("${prefix}_tails.fa.gz") , emit: tails + tuple val("${task.process}"), val('gstama'), eval("tama_collapse.py -version | sed -n 's/tc_version_date_//p'"), emit: versions_gstama, topic: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" if( "$fasta" == "${prefix}.fasta" | "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, set prefix in module configuration" """ tama_flnc_polya_cleanup.py \\ -f $fasta \\ -p ${prefix} \\ $args + gzip ${prefix}.fa gzip ${prefix}_polya_flnc_report.txt gzip ${prefix}_tails.fa + """ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' ) - END_VERSIONS + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.fa.gz + echo "" | gzip > ${prefix}_polya_flnc_report.txt.gz + echo "" | gzip > ${prefix}_tails.fa.gz """ } diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index d8d1754..230613e 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -1,5 +1,6 @@ name: gstama_polyacleanup -description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3) +description: Helper script, remove remaining polyA sequences from Full Length + Non Chimeric reads (Pacbio isoseq3) keywords: - gstama - gstama/polyacleanup @@ -15,39 +16,80 @@ tools: documentation: https://github.com/GenomeRIK/tama/wiki tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" - licence: ["GPL v3 License"] + licence: + - "GPL v3 License" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Full Length Non Chimeric reads in fasta format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Full Length Non Chimeric reads in fasta format + pattern: "*.{fa,fasta}" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip. - pattern: "*_tama.fa.gz" - - report: - type: file - description: A text file describing the number of polyA tails removed and their length. Compressed with gzip. - pattern: "*_tama_polya_flnc_report.txt.gz" - - tails: - type: file - description: A gzip compressed FASTA file of trimmed polyA tails. - pattern: "*_tama_tails.fa.gz" + fasta: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.fa.gz": + type: file + description: The Full Length Non Chimeric reads cleaned from remaining + polyA tails. The sequences are in FASTA format compressed with gzip. + pattern: "*.fa.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}_polya_flnc_report.txt.gz": + type: file + description: A text file describing the number of polyA tails removed + and their length. Compressed with gzip. + pattern: "*_polya_flnc_report.txt.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP + tails: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}_tails.fa.gz": + type: file + description: A gzip compressed FASTA file of trimmed polyA tails. + pattern: "*_tails.fa.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP + versions_gstama: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_collapse.py -version | sed -n 's/tc_version_date_//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gstama: + type: string + description: The name of the tool + - tama_collapse.py -version | sed -n 's/tc_version_date_//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test new file mode 100644 index 0000000..6296b10 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test @@ -0,0 +1,55 @@ + +nextflow_process { + + name "Test Process GSTAMA_POLYACLEANUP" + script "../main.nf" + process "GSTAMA_POLYACLEANUP" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/polyacleanup" + + test("test-gstama-polyacleanup") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-gstama-polyacleanup -- stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + +} diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap new file mode 100644 index 0000000..7adfc42 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap @@ -0,0 +1,86 @@ +{ + "test-gstama-polyacleanup": { + "content": [ + { + "fasta": [ + [ + { + "id": "test" + }, + "test.fa.gz:md5,f0a2c3ca8f19d2197c6b5b273093ebf0" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test_polya_flnc_report.txt.gz:md5,83ba9d11a59ff516f45dd45c78613206" + ] + ], + "tails": [ + [ + { + "id": "test" + }, + "test_tails.fa.gz:md5,20a02db3d29cc45b39880e1ad5ee243b" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_POLYACLEANUP", + "gstama", + "2021_11_03" + ] + ] + } + ], + "timestamp": "2026-07-29T15:42:39.619928488", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test-gstama-polyacleanup -- stub": { + "content": [ + { + "fasta": [ + [ + { + "id": "test" + }, + "test.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test_polya_flnc_report.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tails": [ + [ + { + "id": "test" + }, + "test_tails.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_gstama": [ + [ + "GSTAMA_POLYACLEANUP", + "gstama", + "2021_11_03" + ] + ] + } + ], + "timestamp": "2026-07-29T15:42:48.519457766", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index dfc02a7..9b926b1 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,9 +1,12 @@ -name: gunzip +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: + - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 5e67e3b..6edffc5 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -1,55 +1,47 @@ process GUNZIP { - tag "$archive" + tag "${archive}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : - 'nf-core/ubuntu:22.04' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(archive) output: - tuple val(meta), path("$gunzip"), emit: gunzip - path "versions.yml" , emit: versions + tuple val(meta), path("${gunzip}"), emit: gunzip + tuple val("${task.process}"), val('gunzip'), eval('gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//"'), topic: versions, emit: versions_gunzip when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] - def name = archive.toString() - '.gz' - ".$extension" - def prefix = task.ext.prefix ?: name - gunzip = prefix + ".$extension" + def args = task.ext.args ?: '' + def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".${extension}" """ # Not calling gunzip itself because it creates files # with the original group ownership rather than the # default one for that user / the work directory gzip \\ -cd \\ - $args \\ - $archive \\ - > $gunzip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') - END_VERSIONS + ${args} \\ + ${archive} \\ + > ${gunzip} """ stub: - def args = task.ext.args ?: '' - def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] - def name = archive.toString() - '.gz' - ".$extension" - def prefix = task.ext.prefix ?: name - gunzip = prefix + ".$extension" + def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name + def extension = file(nameWithoutGz).extension + def name = file(nameWithoutGz).baseName + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".${extension}" """ - touch $gunzip - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') - END_VERSIONS + touch ${gunzip} """ } diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a..bba6b3b 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,53 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" + ontologies: [] output: - - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + gunzip: + - - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + ontologies: [] + - ${gunzip}: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + ontologies: [] + versions_gunzip: + - - ${task.process}: + type: string + description: The process the versions were collected from + - gunzip: + type: string + description: The tool name + - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - gunzip: + type: string + description: The tool name + - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test index 776211a..33cb75a 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -89,6 +89,60 @@ nextflow_process { } + test("Should decompress file with extension appearing multiple times in filename") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true).copyTo('test.fa.v1.fa.gz') + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.gunzip[0][1]).name == 'test.fa.v1.fa' } + ) + } + + } + + test("Should decompress file with extension appearing multiple times in filename - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true).copyTo('test.fa.v1.fa.gz') + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + test("Should run without failures - prefix - stub") { options '-stub' diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap index 069967e..980e95a 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test.snap +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -1,4 +1,45 @@ { + "Should decompress file with extension appearing multiple times in filename - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fa:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fa:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions_gunzip": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] + ] + } + ], + "timestamp": "2026-04-15T15:20:52.59447", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "Should run without failures - prefix - stub": { "content": [ { @@ -11,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + [ + "GUNZIP", + "gunzip", + "1.13" + ] ], "gunzip": [ [ @@ -21,16 +66,20 @@ "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions_gunzip": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] ] } ], + "timestamp": "2026-01-19T17:21:56.633550769", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T11:35:10.861293" + "nf-test": "0.9.3", + "nextflow": "25.10.2" + } }, "Should run without failures - stub": { "content": [ @@ -44,7 +93,11 @@ ] ], "1": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + [ + "GUNZIP", + "gunzip", + "1.13" + ] ], "gunzip": [ [ @@ -54,16 +107,20 @@ "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions_gunzip": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] ] } ], + "timestamp": "2026-01-19T17:21:51.435621199", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T11:35:05.857145" + "nf-test": "0.9.3", + "nextflow": "25.10.2" + } }, "Should run without failures": { "content": [ @@ -77,7 +134,11 @@ ] ], "1": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + [ + "GUNZIP", + "gunzip", + "1.13" + ] ], "gunzip": [ [ @@ -87,16 +148,20 @@ "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" ] ], - "versions": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions_gunzip": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] ] } ], + "timestamp": "2026-01-19T17:21:40.613975821", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2023-10-17T15:35:37.690477896" + "nf-test": "0.9.3", + "nextflow": "25.10.2" + } }, "Should run without failures - prefix": { "content": [ @@ -110,7 +175,11 @@ ] ], "1": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + [ + "GUNZIP", + "gunzip", + "1.13" + ] ], "gunzip": [ [ @@ -120,15 +189,19 @@ "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" ] ], - "versions": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions_gunzip": [ + [ + "GUNZIP", + "gunzip", + "1.13" + ] ] } ], + "timestamp": "2026-01-19T17:21:46.086880414", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T11:33:32.921739" + "nf-test": "0.9.3", + "nextflow": "25.10.2" + } } } \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml deleted file mode 100644 index fd3f691..0000000 --- a/modules/nf-core/gunzip/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gunzip: - - modules/nf-core/gunzip/** diff --git a/modules/nf-core/isoseq/refine/environment.yml b/modules/nf-core/isoseq/refine/environment.yml index 05fb46f..7be3253 100644 --- a/modules/nf-core/isoseq/refine/environment.yml +++ b/modules/nf-core/isoseq/refine/environment.yml @@ -1,7 +1,7 @@ -name: isoseq_refine +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::isoseq=4.0.0 diff --git a/modules/nf-core/isoseq/refine/main.nf b/modules/nf-core/isoseq/refine/main.nf index 63bcf5e..68d6d86 100644 --- a/modules/nf-core/isoseq/refine/main.nf +++ b/modules/nf-core/isoseq/refine/main.nf @@ -3,9 +3,9 @@ process ISOSEQ_REFINE { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/isoseq:4.0.0--h9ee0642_0' : - 'biocontainers/isoseq:4.0.0--h9ee0642_0' }" + 'quay.io/biocontainers/isoseq:4.0.0--h9ee0642_0' }" input: tuple val(meta), path(bam) @@ -17,7 +17,7 @@ process ISOSEQ_REFINE { tuple val(meta), path("*.consensusreadset.xml") , emit: consensusreadset tuple val(meta), path("*.filter_summary.report.json"), emit: summary tuple val(meta), path("*.report.csv") , emit: report - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('isoseq'), eval("isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//'"), emit: versions_isoseq, topic: versions when: task.ext.when == null || task.ext.when @@ -33,26 +33,15 @@ process ISOSEQ_REFINE { $bam \\ $primers \\ ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - isoseq: \$( isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' ) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch dummy.bam - touch dummy.bam.pbi - touch dummy.consensusreadset.xml - touch dummy.filter_summary.report.json - touch dummy.report.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - isoseq: \$( isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' ) - END_VERSIONS + touch ${prefix}.bam + touch ${prefix}.bam.pbi + touch ${prefix}.consensusreadset.xml + touch ${prefix}.filter_summary.report.json + touch ${prefix}.report.csv """ } diff --git a/modules/nf-core/isoseq/refine/meta.yml b/modules/nf-core/isoseq/refine/meta.yml index 40f6c4b..de9874b 100644 --- a/modules/nf-core/isoseq/refine/meta.yml +++ b/modules/nf-core/isoseq/refine/meta.yml @@ -12,51 +12,108 @@ tools: homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md - licence: ["BSD-3-Clause-Clear"] + licence: + - "BSD-3-Clause-Clear" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test ] - - bam: - type: file - description: BAM file, cleaned ccs generated by lima - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test ] + - bam: + type: file + description: BAM file, cleaned ccs generated by lima + pattern: "*.bam" + ontologies: [] - primers: type: file description: fasta file of primers pattern: "*.fasta" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: Set of complete reads (with polyA tail), where the polyA has been trimmed - pattern: "*.bam" - - pbi: - type: file - description: Pacbio index file from polyA trimmed reads - pattern: "*.pbi" - - consensusreadset: - type: file - description: Metadata about read library - pattern: "*.xml" - - summary: - type: file - description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads - pattern: "*.json" - - report: - type: file - description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name) - pattern: "*.csv" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: Set of complete reads (with polyA tail), where the polyA has + been trimmed + pattern: "*.bam" + ontologies: [] + pbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file from polyA trimmed reads + pattern: "*.pbi" + ontologies: [] + consensusreadset: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.consensusreadset.xml": + type: file + description: Metadata about read library + pattern: "*.xml" + ontologies: + - edam: http://edamontology.org/format_2332 + summary: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.filter_summary.report.json": + type: file + description: json file describing number of full length reads, full length + non chimeric reads and full length non chimeric polyA reads + pattern: "*.json" + ontologies: + - edam: http://edamontology.org/format_3464 + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report.csv": + type: file + description: Metadata about primer and polyA detection (primers/polyA/insert + length, strand, primer name) + pattern: "*.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + versions_isoseq: + - - ${task.process}: + type: string + description: The name of the process + - isoseq: + type: string + description: The name of the tool + - isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\+//': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - isoseq: + type: string + description: The name of the tool + - isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\+//': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/isoseq/refine/tests/main.nf.test b/modules/nf-core/isoseq/refine/tests/main.nf.test index b1c7dda..71063b1 100644 --- a/modules/nf-core/isoseq/refine/tests/main.nf.test +++ b/modules/nf-core/isoseq/refine/tests/main.nf.test @@ -27,12 +27,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.bam).match("bam") }, - { assert snapshot(process.out.pbi).match("pbi") }, + { assert snapshot( + process.out.bam, + process.out.pbi, + process.out.report, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, { assert path(process.out.consensusreadset.get(0).get(1)).text.contains("PacBio.DataSet.ConsensusReadSet") }, { assert path(process.out.summary.get(0).get(1)).text.contains("pbcopper") }, - { assert snapshot(process.out.report).match("report") }, - { assert snapshot(process.out.versions).match("versions") } ) } } @@ -56,7 +58,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/isoseq/refine/tests/main.nf.test.snap b/modules/nf-core/isoseq/refine/tests/main.nf.test.snap index 62da630..a5b6ab2 100644 --- a/modules/nf-core/isoseq/refine/tests/main.nf.test.snap +++ b/modules/nf-core/isoseq/refine/tests/main.nf.test.snap @@ -1,56 +1,55 @@ { - "PacBio isoseq refine - Chimeras Removing test - stub": { + "PacBio isoseq refine - Chimeras Removing test": { "content": [ + [ + [ + { + "id": "test" + }, + "test.refine.bam:md5,4a666931c2c8843d8a8f0d901e1ba15f" + ] + ], + [ + [ + { + "id": "test" + }, + "test.refine.bam.pbi:md5,fcd3c9b9c7efea71732591ff1271a3b5" + ] + ], + [ + [ + { + "id": "test" + }, + "test.refine.report.csv:md5,d42a139e5d9b08396bdb087c01243ea9" + ] + ], { - "0": [ - [ - { - "id": "test" - }, - "dummy.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ + "versions_isoseq": [ [ - { - "id": "test" - }, - "dummy.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "ISOSEQ_REFINE", + "isoseq", + "4.0.0" ] - ], - "2": [ - [ - { - "id": "test" - }, - "dummy.consensusreadset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "dummy.filter_summary.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - { - "id": "test" - }, - "dummy.report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" - ], + ] + } + ], + "timestamp": "2026-06-03T14:05:40.492223379", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "PacBio isoseq refine - Chimeras Removing test - stub": { + "content": [ + { "bam": [ [ { "id": "test" }, - "dummy.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.refine.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "consensusreadset": [ @@ -58,7 +57,7 @@ { "id": "test" }, - "dummy.consensusreadset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.refine.consensusreadset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "pbi": [ @@ -66,7 +65,7 @@ { "id": "test" }, - "dummy.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.refine.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report": [ @@ -74,7 +73,7 @@ { "id": "test" }, - "dummy.report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.refine.report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "summary": [ @@ -82,81 +81,22 @@ { "id": "test" }, - "dummy.filter_summary.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.refine.filter_summary.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" + "versions_isoseq": [ + [ + "ISOSEQ_REFINE", + "isoseq", + "4.0.0" + ] ] } ], + "timestamp": "2026-06-03T14:05:45.050914829", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T22:41:31.59497" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-14T10:40:47.708497" - }, - "pbi": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.refine.bam.pbi:md5,fcd3c9b9c7efea71732591ff1271a3b5" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-14T10:34:21.23301" - }, - "report": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.refine.report.csv:md5,d42a139e5d9b08396bdb087c01243ea9" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-14T10:34:21.292332" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.refine.bam:md5,4a666931c2c8843d8a8f0d901e1ba15f" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-14T10:34:21.174269" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/isoseq/refine/tests/nextflow.config b/modules/nf-core/isoseq/refine/tests/nextflow.config index 3c49ec7..09a63ab 100644 --- a/modules/nf-core/isoseq/refine/tests/nextflow.config +++ b/modules/nf-core/isoseq/refine/tests/nextflow.config @@ -1,6 +1,5 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } ext.prefix = { "${meta.id}.refine" } } diff --git a/modules/nf-core/isoseq/refine/tests/tags.yml b/modules/nf-core/isoseq/refine/tests/tags.yml deleted file mode 100644 index c6f3ffb..0000000 --- a/modules/nf-core/isoseq/refine/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -isoseq/refine: - - modules/nf-core/isoseq/refine/** diff --git a/modules/nf-core/lima/environment.yml b/modules/nf-core/lima/environment.yml index a9718bc..2e56e30 100644 --- a/modules/nf-core/lima/environment.yml +++ b/modules/nf-core/lima/environment.yml @@ -1,7 +1,8 @@ -name: lima +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::lima=2.9.0 + - bioconda::lima=2.12.0 diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index e44fdda..7b860ff 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -3,9 +3,9 @@ process LIMA { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/lima:2.9.0--h9ee0642_1' : - 'biocontainers/lima:2.9.0--h9ee0642_1' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/lima:2.12.0--h9ee0642_1' : + 'quay.io/biocontainers/lima:2.12.0--h9ee0642_1' }" input: tuple val(meta), path(ccs) @@ -15,12 +15,12 @@ process LIMA { tuple val(meta), path("*.counts") , emit: counts tuple val(meta), path("*.report") , emit: report tuple val(meta), path("*.summary"), emit: summary - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('lima'), eval("lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'"), emit: versions_lima, topic: versions tuple val(meta), path("*.bam") , optional: true, emit: bam tuple val(meta), path("*.bam.pbi") , optional: true, emit: pbi - tuple val(meta), path("*.{fa, fasta}") , optional: true, emit: fasta - tuple val(meta), path("*.{fa.gz, fasta.gz}"), optional: true, emit: fastagz + tuple val(meta), path("*.{fa,fasta}") , optional: true, emit: fasta + tuple val(meta), path("*.{fa.gz,fasta.gz}"), optional: true, emit: fastagz tuple val(meta), path("*.fastq") , optional: true, emit: fastq tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz tuple val(meta), path("*.xml") , optional: true, emit: xml @@ -61,24 +61,12 @@ process LIMA { $prefix.\$OUT_EXT \\ -j $task.cpus \\ $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - lima: \$( lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g' ) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" """ touch dummy.counts touch dummy.report touch dummy.summary - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - lima: \$( lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g' ) - END_VERSIONS """ } diff --git a/modules/nf-core/lima/meta.yml b/modules/nf-core/lima/meta.yml index ad4ebbf..74ed46d 100644 --- a/modules/nf-core/lima/meta.yml +++ b/modules/nf-core/lima/meta.yml @@ -13,82 +13,198 @@ tools: documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - ccs: - type: file - description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs - pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ccs: + type: file + description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads + or ccs + pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ - primers: type: file description: Fasta file, sequences of primers pattern: "*.fasta" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A bam file of ccs purged of primers - pattern: "*.bam" - - pbi: - type: file - description: Pacbio index file of ccs purged of primers - pattern: "*.bam" - - xml: - type: file - description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads. - pattern: "*.xml" - - json: - type: file - description: A metadata json file - pattern: "*.json" - - clips: - type: file - description: A fasta file of clipped primers - pattern: "*.clips" - - counts: - type: file - description: A tabulated file of describing pairs of primers - pattern: "*.counts" - - guess: - type: file - description: A second tabulated file of describing pairs of primers (no doc available) - pattern: "*.guess" - - report: - type: file - description: A tab-separated file about each ZMW, unfiltered - pattern: "*.report" - - summary: - type: file - description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered. - pattern: "*.summary" - - fasta: - type: file - description: A fasta file of ccs purged of primers. - pattern: "*.fa" - - fastagz: - type: file - description: A fasta.gz file of ccs purged of primers. - pattern: "*.fasta.gz" - - fastq: - type: file - description: A fastq file of ccs purged of primers. - pattern: "*.fastq" - - fastqgz: - type: file - description: A fastq.gz file of ccs purged of primers. - pattern: "*.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + counts: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.counts": + type: file + description: A tabulated file of describing pairs of primers + pattern: "*.counts" + ontologies: [] + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report": + type: file + description: A tab-separated file about each ZMW, unfiltered + pattern: "*.report" + ontologies: [] + summary: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.summary": + type: file + description: This file shows how many ZMWs have been filtered, how ZMWs many + are same/different, and how many reads have been filtered. + pattern: "*.summary" + ontologies: [] + versions_lima: + - - ${task.process}: + type: string + description: The process the versions were collected from + - lima: + type: string + description: The tool name + - "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": + type: string + description: The command used to generate the version of the tool + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: A bam file of ccs purged of primers + pattern: "*.bam" + ontologies: [] + pbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file of ccs purged of primers + pattern: "*.bam" + ontologies: [] + fasta: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa,fasta}": + type: file + description: A fasta file of ccs purged of primers. + pattern: "*.fa" + ontologies: [] + fastagz: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa.gz,fasta.gz}": + type: file + description: A fasta.gz file of ccs purged of primers. + pattern: "*.fasta.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + fastq: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq": + type: file + description: A fastq file of ccs purged of primers. + pattern: "*.fastq" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + fastqgz: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq.gz": + type: file + description: A fastq.gz file of ccs purged of primers. + pattern: "*.fastq.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + xml: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xml": + type: file + description: An XML file representing a set of a particular sequence data + type such as subreads, references or aligned subreads. + pattern: "*.xml" + ontologies: + - edam: http://edamontology.org/format_2332 # XML + json: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: A metadata json file + pattern: "*.json" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + clips: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.clips": + type: file + description: A fasta file of clipped primers + pattern: "*.clips" + ontologies: [] + guess: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.guess": + type: file + description: A second tabulated file of describing pairs of primers (no doc + available) + pattern: "*.guess" + ontologies: [] +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - lima: + type: string + description: The tool name + - "lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g'": + type: string + description: The command used to generate the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/lima/tests/main.nf.test b/modules/nf-core/lima/tests/main.nf.test index bf7d22c..89cc392 100644 --- a/modules/nf-core/lima/tests/main.nf.test +++ b/modules/nf-core/lima/tests/main.nf.test @@ -29,7 +29,7 @@ nextflow_process { { assert snapshot(process.out.counts).match("counts") }, { assert snapshot(process.out.report).match("report") }, { assert snapshot(process.out.summary).match("summary") }, - { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, { assert snapshot(process.out.bam).match("bam") }, { assert snapshot(process.out.pbi).match("pbi") }, { assert snapshot(process.out.fasta).match("fasta") }, @@ -66,7 +66,7 @@ nextflow_process { } - test("LIMA - Primer Removal - Input => fa.gz") { + test("LIMA - Primer Removal - Input => fa.gz") { when { process { diff --git a/modules/nf-core/lima/tests/main.nf.test.snap b/modules/nf-core/lima/tests/main.nf.test.snap index f64e3dc..3e39169 100644 --- a/modules/nf-core/lima/tests/main.nf.test.snap +++ b/modules/nf-core/lima/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "summary": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,bcbcaaaca418bdeb91141c81715ca420" + ] + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2026-02-12T12:34:25.47480559" + }, + "LIMA - Primer Removal - Input => bam": { + "content": [ + { + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2026-02-12T12:34:25.504600431" + }, "fastqgz": { "content": [ [ @@ -6,10 +41,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:01.98256" + "timestamp": "2026-02-12T12:34:25.885991815" }, "counts": { "content": [ @@ -23,10 +58,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:00.491188" + "timestamp": "2026-02-12T12:34:25.40513167" }, "clips": { "content": [ @@ -40,10 +75,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:02.19417" + "timestamp": "2026-02-12T12:34:25.951132172" }, "LIMA - Primer Removal - Input => fq.gz - stub": { "content": [ @@ -85,7 +120,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ @@ -156,8 +195,12 @@ "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -165,10 +208,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:43.376049" + "timestamp": "2026-02-12T12:35:52.451468526" }, "LIMA - Primer Removal - Input => fq.gz": { "content": [ @@ -220,7 +263,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ [ @@ -331,8 +378,12 @@ "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -340,10 +391,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:13.306885" + "timestamp": "2026-02-12T12:35:15.500956685" }, "LIMA - Primer Removal - Input => fq": { "content": [ @@ -395,7 +446,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ [ @@ -506,8 +561,12 @@ "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -515,10 +574,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:07.559264" + "timestamp": "2026-02-12T12:35:03.038935069" }, "LIMA - Primer Removal - Input => fa.gz - stub": { "content": [ @@ -560,7 +619,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ @@ -631,8 +694,12 @@ "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -640,10 +707,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:30.69067" + "timestamp": "2026-02-12T12:35:37.745197933" }, "fasta": { "content": [ @@ -652,56 +719,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:01.262691" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,d3de1934aa8fb39e961345916b3ae57b" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-17T11:35:00.822221" - }, - "fastq": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-17T11:35:01.752773" - }, - "summary": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.fl.lima.summary:md5,bcbcaaaca418bdeb91141c81715ca420" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-17T11:35:00.704932" + "timestamp": "2026-02-12T12:34:25.681651786" }, "LIMA - Primer Removal - Input => fq - stub": { "content": [ @@ -743,7 +764,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ @@ -814,8 +839,12 @@ "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -823,10 +852,27 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:37.019064" + "timestamp": "2026-02-12T12:35:45.365210245" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,59b04f200c309b0a60a3f182d22f6910" + ] + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2026-02-12T12:34:25.523508284" }, "LIMA - Primer Removal - Input => bam - stub": { "content": [ @@ -868,7 +914,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ @@ -939,8 +989,12 @@ "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -948,10 +1002,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:18.958286" + "timestamp": "2026-02-12T12:35:22.965691216" }, "LIMA - Primer Removal - Input => fa - stub": { "content": [ @@ -993,7 +1047,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ @@ -1064,8 +1122,12 @@ "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -1073,10 +1135,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:25.020259" + "timestamp": "2026-02-12T12:35:30.433815019" }, "fastagz": { "content": [ @@ -1085,22 +1147,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-17T11:35:01.493258" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:00.76398" + "timestamp": "2026-02-12T12:34:25.749681972" }, "guess": { "content": [ @@ -1114,10 +1164,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:02.396472" + "timestamp": "2026-02-12T12:34:26.026327633" }, "pbi": { "content": [ @@ -1126,15 +1176,15 @@ { "id": "test" }, - "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,b531dcf8afc5f6c1caf40c7affb6a90c" + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,851cf26eb54e4399cba5241db969dc0c" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:01.042955" + "timestamp": "2026-02-12T12:34:25.612906854" }, "report": { "content": [ @@ -1148,10 +1198,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-01-17T11:35:00.626772" + "timestamp": "2026-02-12T12:34:25.422692879" }, "LIMA - Primer Removal - Input => fa": { "content": [ @@ -1203,7 +1253,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ [ @@ -1222,7 +1276,12 @@ ] ], "6": [ - + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fasta:md5,d4eea419961c205ef84ef39176e30ef3" + ] ], "7": [ @@ -1258,7 +1317,12 @@ ] ], "fasta": [ - + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fasta:md5,d4eea419961c205ef84ef39176e30ef3" + ] ], "fastagz": [ @@ -1304,8 +1368,12 @@ "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -1313,10 +1381,22 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:46:54.854736" + "timestamp": "2026-02-12T12:34:38.412905201" + }, + "fastq": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2026-02-12T12:34:25.819717953" }, "LIMA - Primer Removal - Input => fa.gz": { "content": [ @@ -1368,7 +1448,11 @@ ] ], "3": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + [ + "LIMA", + "lima", + "2.12.0" + ] ], "4": [ [ @@ -1390,7 +1474,12 @@ ], "7": [ - + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fasta.gz:md5,d4eea419961c205ef84ef39176e30ef3" + ] ], "8": [ @@ -1426,7 +1515,12 @@ ], "fastagz": [ - + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fasta.gz:md5,d4eea419961c205ef84ef39176e30ef3" + ] ], "fastq": [ @@ -1469,8 +1563,12 @@ "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" ] ], - "versions": [ - "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + "versions_lima": [ + [ + "LIMA", + "lima", + "2.12.0" + ] ], "xml": [ @@ -1478,9 +1576,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-05-13T08:47:01.506833" + "timestamp": "2026-02-12T12:34:50.42113371" } } \ No newline at end of file diff --git a/modules/nf-core/lima/tests/tags.yml b/modules/nf-core/lima/tests/tags.yml deleted file mode 100644 index bf24add..0000000 --- a/modules/nf-core/lima/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -lima: - - modules/nf-core/lima/** diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml index 41e8fe9..d8135f9 100644 --- a/modules/nf-core/minimap2/align/environment.yml +++ b/modules/nf-core/minimap2/align/environment.yml @@ -1,11 +1,9 @@ -name: minimap2_align - +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::htslib=1.20 - - bioconda::minimap2=2.28 - - bioconda::samtools=1.20 + - bioconda::minimap2=2.30 + - bioconda::samtools=1.23.1 diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf index d82dc14..e61e77e 100644 --- a/modules/nf-core/minimap2/align/main.nf +++ b/modules/nf-core/minimap2/align/main.nf @@ -4,9 +4,9 @@ process MINIMAP2_ALIGN { // Note: the versions here need to match the versions used in the mulled container below and minimap2/index conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0' : - 'biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/37671219cfd244eb9b33db9345d3543ffd83037419a1c57f4648aace493ec2c2/data' : + 'community.wave.seqera.io/library/minimap2_samtools:b09096fc890429ce' }" input: tuple val(meta), path(reads) @@ -20,7 +20,7 @@ process MINIMAP2_ALIGN { tuple val(meta), path("*.paf") , optional: true, emit: paf tuple val(meta), path("*.bam") , optional: true, emit: bam tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("minimap2"), eval("minimap2 --version"), topic: versions, emit: versions_minimap2 when: task.ext.when == null || task.ext.when @@ -38,25 +38,17 @@ process MINIMAP2_ALIGN { def bam_input = "${reads.extension}".matches('sam|bam|cram') def samtools_reset_fastq = bam_input ? "samtools reset --threads ${task.cpus-1} $args3 $reads | samtools fastq --threads ${task.cpus-1} $args4 |" : '' def query = bam_input ? "-" : reads - def target = reference ?: (bam_input ? error("BAM input requires reference") : reads) - + def target = reference ?: (bam_input ? error("Error: minimap2/align BAM input mode requires reference") : reads) """ $samtools_reset_fastq \\ minimap2 \\ - $args \\ - -t $task.cpus \\ - $target \\ - $query \\ - $cigar_paf \\ - $set_cigar_bam \\ - $bam_output - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - minimap2: \$(minimap2 --version 2>&1) - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + ${args} \\ + -t ${task.cpus} \\ + ${target} \\ + ${query} \\ + ${cigar_paf} \\ + ${set_cigar_bam} \\ + ${bam_output} """ stub: @@ -64,15 +56,11 @@ process MINIMAP2_ALIGN { def output_file = bam_format ? "${prefix}.bam" : "${prefix}.paf" def bam_index = bam_index_extension ? "touch ${prefix}.bam.${bam_index_extension}" : "" def bam_input = "${reads.extension}".matches('sam|bam|cram') - def target = reference ?: (bam_input ? error("BAM input requires reference") : reads) - + if(bam_input && !reference) { + error("Error: minimap2/align BAM input mode requires reference!") + } """ touch $output_file ${bam_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - minimap2: \$(minimap2 --version 2>&1) - END_VERSIONS """ } diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml index 8996f88..40bb20a 100644 --- a/modules/nf-core/minimap2/align/meta.yml +++ b/modules/nf-core/minimap2/align/meta.yml @@ -14,26 +14,29 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_ref'] - - reference: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_ref'] + - reference: + type: file + description: | + Reference database in FASTA format. + ontologies: [] - bam_format: type: boolean description: Specify that output should be in BAM format @@ -49,27 +52,60 @@ input: Write CIGAR with >65535 ops at the CG tag. This is recommended when doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" - - bam: - type: file - description: Alignment in BAM format - pattern: "*.bam" - - index: - type: file - description: BAM alignment index - pattern: "*.bam.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + paf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" + ontologies: [] + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Alignment in BAM format + pattern: "*.bam" + ontologies: [] + index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.${bam_index_extension}": + type: file + description: BAM alignment index + pattern: "*.bam.*" + ontologies: [] + versions_minimap2: + - - ${task.process}: + type: string + description: The process name + - minimap2: + type: string + description: The tool name + - minimap2 --version: + type: eval + description: The tool version +topics: + versions: + - - ${task.process}: + type: string + description: The process name + - minimap2: + type: string + description: The tool name + - minimap2 --version: + type: eval + description: The tool version authors: - "@heuermh" - "@sofstam" diff --git a/modules/nf-core/minimap2/align/tests/main.nf.test b/modules/nf-core/minimap2/align/tests/main.nf.test index 4072c17..34597d6 100644 --- a/modules/nf-core/minimap2/align/tests/main.nf.test +++ b/modules/nf-core/minimap2/align/tests/main.nf.test @@ -36,7 +36,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -71,7 +71,7 @@ nextflow_process { bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.index[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -108,7 +108,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -142,7 +142,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -176,7 +176,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -211,7 +211,7 @@ nextflow_process { bam(process.out.bam[0][1]).getHeader(), bam(process.out.bam[0][1]).getReadsMD5(), file(process.out.index[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions_") } ).match() } ) } @@ -438,4 +438,4 @@ nextflow_process { } -} \ No newline at end of file +} diff --git a/modules/nf-core/minimap2/align/tests/main.nf.test.snap b/modules/nf-core/minimap2/align/tests/main.nf.test.snap index 12264a8..4923727 100644 --- a/modules/nf-core/minimap2/align/tests/main.nf.test.snap +++ b/modules/nf-core/minimap2/align/tests/main.nf.test.snap @@ -4,20 +4,26 @@ [ "@HD\tVN:1.6\tSO:coordinate", "@SQ\tSN:MT192765.1\tLN:29829", - "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta -", - "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index" + "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta -", + "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index" ], "5d426b9a5f5b2c54f1d7f1e4c238ae94", "test.bam.bai", - [ - "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd" - ] + { + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] + ] + } ], + "timestamp": "2026-04-23T17:26:01.315588", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-25T09:03:00.827260362" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - bam, fasta, true, 'bai', false, false - stub": { "content": [ @@ -44,7 +50,11 @@ ] ], "3": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ], "bam": [ [ @@ -67,16 +77,20 @@ "paf": [ ], - "versions": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ] } ], + "timestamp": "2026-04-23T17:26:29.211025", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-23T11:21:37.92353539" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - fastq, fasta, true, 'bai', false, false - stub": { "content": [ @@ -103,7 +117,11 @@ ] ], "3": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ], "bam": [ [ @@ -126,16 +144,20 @@ "paf": [ ], - "versions": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ] } ], + "timestamp": "2026-04-23T17:26:14.56423", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-03T11:29:44.669021368" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - fastq, fasta, false, [], false, false - stub": { "content": [ @@ -156,7 +178,11 @@ ], "3": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ], "bam": [ @@ -173,16 +199,20 @@ "test.paf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ] } ], + "timestamp": "2026-04-23T17:26:19.467028", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-03T11:15:52.738781039" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - fastq, fasta, true, [], false, false - stub": { "content": [ @@ -203,7 +233,11 @@ ], "3": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ], "bam": [ [ @@ -220,93 +254,121 @@ "paf": [ ], - "versions": [ - "versions.yml:md5,98b8f5f36aa54b82210094f0b0d11938" + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] ] } ], + "timestamp": "2026-04-23T17:26:10.208287", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-03T11:15:23.033808223" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - [fastq1, fastq2], fasta, true, false, false": { "content": [ [ "@HD\tVN:1.6\tSO:coordinate", "@SQ\tSN:MT192765.1\tLN:29829", - "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz test_2.fastq.gz", - "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam" + "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz test_2.fastq.gz", + "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam" ], "1bc392244f228bf52cf0b5a8f6a654c9", - [ - "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd" - ] + { + "versions_minimap2": [ + [ + "MINIMAP2_ALIGN", + "minimap2", + "2.30-r1287" + ] + ] + } ], + "timestamp": "2026-04-23T17:25:45.435644", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-23T11:18:18.964586894" + "nf-test": "0.9.5", + "nextflow": "25.04.2" + } }, "sarscov2 - fastq, fasta, true, [], false, false": { "content": [ [ "@HD\tVN:1.6\tSO:coordinate", "@SQ\tSN:MT192765.1\tLN:29829", - "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz", - "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam" + "@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz", + "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam" ], "f194745c0ccfcb2a9c0aee094a08750", - [ - "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd" - ] + { + "versions_minimap2": 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b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,7 @@ -name: multiqc +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index d536580..c4bc715 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,24 +1,21 @@ process MULTIQC { + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.html"), emit: report + tuple val(meta), path("*_data"), emit: data + tuple val(meta), path("*_plots"), emit: plots, optional: true + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions when: task.ext.when == null || task.ext.when @@ -26,38 +23,28 @@ process MULTIQC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data - touch multiqc_plots + touch multiqc_data/.stub + mkdir multiqc_plots + touch multiqc_plots/.stub touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 382c08c..27ce18d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -11,54 +12,91 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*.html": + type: file + description: MultiQC report file + pattern: ".html" + ontologies: [] + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_plots" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -69,3 +107,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt + linux/arm64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt + docker: + linux/amd64: + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 + linux/arm64: + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data + linux/arm64: + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 0000000..b30b135 --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7..4cbdb95 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -15,25 +15,84 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) + """ + } } + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } } test("sarscov2 single-end [fastqc] [config]") { @@ -41,23 +100,85 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] [multiple configs]") { + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [ + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) + ], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -68,25 +189,23 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 83fa080..4489921 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,422 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T12:41:34.562023" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_stub": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T11:27:11.933869532" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] - stub": { "content": [ - [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" - ] + { + "data": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "plots": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "report": [ + [ + { + "id": "FASTQC" + }, + "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-10T11:26:56.709849369" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] [config]": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:30.372239611", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] - custom prefix": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.35" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:18.189023981", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } -} +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config index c537a6a..374dfef 100644 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: 'MULTIQC' { ext.prefix = null + ext.args = '-p' } } diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/modules/nf-core/pbccs/environment.yml b/modules/nf-core/pbccs/environment.yml index bdc662b..6502384 100644 --- a/modules/nf-core/pbccs/environment.yml +++ b/modules/nf-core/pbccs/environment.yml @@ -1,7 +1,7 @@ -name: pbccs +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pbccs=6.4.0 diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index dd2d0ad..54911ce 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -3,9 +3,9 @@ process PBCCS { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbccs:6.4.0--h9ee0642_0' : - 'biocontainers/pbccs:6.4.0--h9ee0642_0' }" + 'quay.io/biocontainers/pbccs:6.4.0--h9ee0642_0' }" input: tuple val(meta), path(bam), path(pbi) @@ -18,7 +18,7 @@ process PBCCS { tuple val(meta), path("*.report.txt" ) , emit: report_txt tuple val(meta), path("*.report.json" ) , emit: report_json tuple val(meta), path("*.metrics.json.gz"), emit: metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('pbccs'), eval("ccs --version 2>&1 | sed '1!d;s/^.*ccs //; s/ .*//'"), topic: versions, emit: versions_pbccs when: task.ext.when == null || task.ext.when @@ -28,35 +28,23 @@ process PBCCS { def prefix = task.ext.prefix ?: "${meta.id}" """ ccs \\ - $bam \\ + ${bam} \\ ${prefix}.chunk${chunk_num}.bam \\ --report-file ${prefix}.chunk${chunk_num}.report.txt \\ --report-json ${prefix}.chunk${chunk_num}.report.json \\ --metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\ - --chunk $chunk_num/$chunk_on \\ - -j $task.cpus \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//') - END_VERSIONS + --chunk ${chunk_num}/${chunk_on} \\ + -j ${task.cpus} \\ + ${args} """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch dummy.chunk1.bam - touch dummy.chunk1.bam.pbi - touch dummy.report.txt - touch dummy.report.json - echo "test" > dummy.metrics.json - gzip dummy.metrics.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//') - END_VERSIONS + touch ${prefix}.chunk1.bam + touch ${prefix}.chunk1.bam.pbi + touch ${prefix}.report.txt + touch ${prefix}.report.json + echo "" | gzip > ${prefix}.metrics.json.gz """ } diff --git a/modules/nf-core/pbccs/meta.yml b/modules/nf-core/pbccs/meta.yml index ded53e0..ad34f9d 100644 --- a/modules/nf-core/pbccs/meta.yml +++ b/modules/nf-core/pbccs/meta.yml @@ -1,5 +1,5 @@ name: pbccs -description: Pacbio ccs - Generate Higly Accurate Single-Molecule Consensus Reads +description: Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads keywords: - ccs - pacbio @@ -11,21 +11,25 @@ tools: homepage: https://github.com/PacificBiosciences/pbbioconda documentation: https://ccs.how/ tool_dev_url: https://github.com/PacificBiosciences/ccs - licence: ["BSD-3-Clause-Clear"] + licence: + - "BSD-3-Clause-Clear" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: id of the split file - - bam: - type: file - description: Raw subreads bam - pattern: "*.subreads.bam" - - pbi: - type: file - description: Pacbio BAM Index - pattern: "*.pbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + id: id of the split file + - bam: + type: file + description: Raw subreads bam + pattern: "*.subreads.bam" + ontologies: [] + - pbi: + type: file + description: Pacbio BAM Index + pattern: "*.pbi" + ontologies: [] - chunk_num: type: integer description: BAM part to process @@ -33,35 +37,87 @@ input: type: integer description: Total number of bam parts to process output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: CCS sequences in bam format - pattern: "*.bam" - - pbi: - type: file - description: PacBio Index of CCS sequences - pattern: "*.pbi" - - report_txt: - type: file - description: Summary of CCS in txt format - pattern: ".txt" - - report_json: - type: file - description: Summary of CCS in txt json - pattern: ".json" - - metrics: - type: file - description: Metrics about zmws - pattern: "*.json.gz" + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam": + type: file + description: CCS sequences in bam format + pattern: "*.bam" + ontologies: [] + pbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam.pbi": + type: file + description: PacBio Index of CCS sequences + pattern: "*.pbi" + ontologies: [] + report_txt: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.report.txt": + type: file + description: CCS report in text format + pattern: "*.report.txt" + ontologies: + - edam: http://edamontology.org/format_2330 # Textual format + report_json: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.report.json": + type: file + description: CCS report in JSON format + pattern: "*.report.json" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + metrics: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json.gz": + type: file + description: Metrics about zmws + pattern: "*.json.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions_pbccs: + - - ${task.process}: + type: string + description: The name of the process + - pbccs: + type: string + description: The name of the tool + - ccs --version 2>&1 | sed '1!d;s/^.*ccs //; s/ .*//': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - pbccs: + type: string + description: The name of the tool + - ccs --version 2>&1 | sed '1!d;s/^.*ccs //; s/ .*//': + type: eval + description: The expression to obtain the version of the tool + authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/pbccs/tests/main.nf.test b/modules/nf-core/pbccs/tests/main.nf.test index ef70d05..d1bf33c 100644 --- a/modules/nf-core/pbccs/tests/main.nf.test +++ b/modules/nf-core/pbccs/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'alz' ], // meta map + [ id:'alz' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true) ] @@ -28,12 +28,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.bam).match("bam") }, - { assert snapshot(process.out.pbi).match("pbi") }, - { assert snapshot(process.out.report_txt).match("report_txt") }, { assert path(process.out.report_json.get(0).get(1)).text.contains("pbcopper") }, { assert path(process.out.metrics.get(0).get(1)).linesGzip.get(0).toString().contains("zmws") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys:["metrics", "report_json"])).match() } ) } @@ -47,7 +44,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'alz' ], // meta map + [ id:'alz' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true) ] @@ -60,7 +57,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/pbccs/tests/main.nf.test.snap b/modules/nf-core/pbccs/tests/main.nf.test.snap index b47348c..4555082 100644 --- a/modules/nf-core/pbccs/tests/main.nf.test.snap +++ b/modules/nf-core/pbccs/tests/main.nf.test.snap @@ -1,102 +1,71 @@ { - "versions": { - "content": [ - [ - "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T08:38:30.999138" - }, - "pbi": { - "content": [ - [ - [ - { - "id": "alz" - }, - "alz.chunk2.bam.pbi:md5,36c3d2843aae90739ee8ca82d27abd55" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T16:37:53.581983" - }, - "report_txt": { - "content": [ - [ - [ - { - "id": "alz" - }, - "alz.chunk2.report.txt:md5,67583febb144333e3f854c7bf4a17a50" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T16:37:53.600993" - }, - "PacBio pbccs - Compute CSS test - stub": { + "PacBio pbccs - Compute CSS test": { "content": [ { - "0": [ + "bam": [ [ { "id": "alz" }, - "dummy.chunk1.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk2.bam:md5,4f99cfdecba7d1d140530608afffa822" ] ], - "1": [ + "metrics": [ [ { "id": "alz" }, - "dummy.chunk1.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk2.metrics.json.gz" ] ], - "2": [ + "pbi": [ [ { "id": "alz" }, - "dummy.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk2.bam.pbi:md5,2a8630a2a6f58cb65ecb9c1c1ff705fb" ] ], - "3": [ + "report_json": [ [ { "id": "alz" }, - "dummy.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk2.report.json" ] ], - "4": [ + "report_txt": [ [ { "id": "alz" }, - "dummy.metrics.json.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + "alz.chunk2.report.txt:md5,67583febb144333e3f854c7bf4a17a50" ] ], - "5": [ - "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" - ], + "versions_pbccs": [ + [ + "PBCCS", + "pbccs", + "6.4.0" + ] + ] + } + ], + "timestamp": "2026-08-04T11:54:37.539447047", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "PacBio pbccs - Compute CSS test - stub": { + "content": [ + { "bam": [ [ { "id": "alz" }, - "dummy.chunk1.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk1.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metrics": [ @@ -104,7 +73,7 @@ { "id": "alz" }, - "dummy.metrics.json.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + "alz.metrics.json.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "pbi": [ @@ -112,7 +81,7 @@ { "id": "alz" }, - "dummy.chunk1.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.chunk1.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_json": [ @@ -120,7 +89,7 @@ { "id": "alz" }, - "dummy.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "report_txt": [ @@ -128,35 +97,22 @@ { "id": "alz" }, - "dummy.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "alz.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" + "versions_pbccs": [ + [ + "PBCCS", + "pbccs", + "6.4.0" + ] ] } ], + "timestamp": "2026-08-04T11:50:21.212231706", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T10:24:03.471175" - }, - "bam": { - "content": [ - [ - [ - { - "id": "alz" - }, - "alz.chunk2.bam:md5,306ba0287e3c7f4cd8f5af577af7ac62" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-13T16:37:53.559407" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/modules/nf-core/pbccs/tests/nextflow.config b/modules/nf-core/pbccs/tests/nextflow.config index 2c2b4fe..5137912 100644 --- a/modules/nf-core/pbccs/tests/nextflow.config +++ b/modules/nf-core/pbccs/tests/nextflow.config @@ -1,3 +1,5 @@ process { - ext.args = '--min-rq 0.9' + withName: 'PBCCS' { + ext.args = '--min-rq 0.9' + } } diff --git a/modules/nf-core/pbccs/tests/tags.yml b/modules/nf-core/pbccs/tests/tags.yml deleted file mode 100644 index 6021606..0000000 --- a/modules/nf-core/pbccs/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pbccs: - - modules/nf-core/pbccs/** diff --git a/modules/nf-core/ultra/align/environment.yml b/modules/nf-core/ultra/align/environment.yml index 74ccba4..4bba7fd 100644 --- a/modules/nf-core/ultra/align/environment.yml +++ b/modules/nf-core/ultra/align/environment.yml @@ -1,8 +1,9 @@ -name: ultra_align +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::ultra_bioinformatics=0.1 - bioconda::samtools=1.17 + - bioconda::ultra_bioinformatics=0.1 diff --git a/modules/nf-core/ultra/align/main.nf b/modules/nf-core/ultra/align/main.nf index b6eb00e..ee2c627 100644 --- a/modules/nf-core/ultra/align/main.nf +++ b/modules/nf-core/ultra/align/main.nf @@ -3,25 +3,26 @@ process ULTRA_ALIGN { label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:c2c0cd48e7ed1cf3f365b421c7389d04e6bfa812-0': - 'biocontainers/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:c2c0cd48e7ed1cf3f365b421c7389d04e6bfa812-0' }" + 'quay.io/biocontainers/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:c2c0cd48e7ed1cf3f365b421c7389d04e6bfa812-0' }" input: tuple val(meta), path(reads) - path genome - tuple path(pickle), path(db) + tuple val(meta2), path(genome) + tuple val(meta3), path(pickle), path(db) output: tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('ultra'), eval("uLTRA --version | sed 's/uLTRA //'"), emit: versions_ultra, topic: versions + tuple val("${task.process}"), val('samtools'), eval("samtools --version | sed -n '1s/samtools //p'"), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ uLTRA \\ @@ -43,11 +44,11 @@ process ULTRA_ALIGN { ${prefix}.sam rm ${prefix}.sam + """ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ultra: \$( uLTRA --version|sed 's/uLTRA //g' ) - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam """ } diff --git a/modules/nf-core/ultra/align/meta.yml b/modules/nf-core/ultra/align/meta.yml index 264e9ab..a1dce39 100644 --- a/modules/nf-core/ultra/align/meta.yml +++ b/modules/nf-core/ultra/align/meta.yml @@ -1,5 +1,6 @@ name: "ultra_align" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome +description: uLTRA aligner - A wrapper around minimap2 to improve small exon + detection - Map reads on genome keywords: - uLTRA - align @@ -14,43 +15,99 @@ tools: documentation: "https://github.com/ksahlin/uLTRA" tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" - licence: "['GNU GPLV3']" + licence: + - "GNU GPLV3" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A fasta or fastq file of reads to align - pattern: "*.{fa,fasta,fastq}" - - genome: - type: file - description: A fasta file of reference genome - pattern: "*.{fa,fasta}" - - pickle: - type: file - description: Pickle files generated by uLTRA index - pattern: "*.pickle" - - db: - type: file - description: Database generated by uLTRA index - pattern: "*.db" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A fasta or fastq file of reads to align + pattern: "*.{fa,fasta,fastq}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test' ] + - genome: + type: file + description: A fasta file of reference genome + pattern: "*.{fa,fasta}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test' ] + - pickle: + type: file + description: Pickle files generated by uLTRA index + pattern: "*.pickle" + ontologies: + - edam: http://edamontology.org/format_4002 # pickle + - db: + type: file + description: Database generated by uLTRA index + pattern: "*.db" + ontologies: [] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: The aligned reads in bam format - pattern: "*.bam" + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: The aligned reads in bam format + pattern: "*.bam" + ontologies: [] + versions_ultra: + - - ${task.process}: + type: string + description: The name of the process + - ultra: + type: string + description: The name of the tool + - uLTRA --version | sed 's/uLTRA //': + type: eval + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version | sed -n '1s/samtools //p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - ultra: + type: string + description: The name of the tool + - uLTRA --version | sed 's/uLTRA //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version | sed -n '1s/samtools //p': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/align/tests/main.nf.test b/modules/nf-core/ultra/align/tests/main.nf.test new file mode 100644 index 0000000..d378013 --- /dev/null +++ b/modules/nf-core/ultra/align/tests/main.nf.test @@ -0,0 +1,112 @@ +nextflow_process { + + name "Test Process ULTRA_ALIGN" + config "./nextflow.config" + script "../main.nf" + process "ULTRA_ALIGN" + + tag "modules" + tag "modules_nfcore" + tag "gunzip" + tag "gnu" + tag "gnu/sort" + tag "ultra" + tag "ultra/index" + tag "ultra/align" + + test("ultra_align") { + setup { + run("GUNZIP") { + script "../../../gunzip/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists:true) + ] + """ + } + } + + run("GNU_SORT") { + script "../../../gnu/sort/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true), + "gtf" + ] + """ + } + } + + run("ULTRA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'fasta'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[1] = GNU_SORT.out.sorted + """ + } + } + } + when { + params { + gnu_sort_args = '-k1,1 -k4,4n' + ultra_index_args = '--disable_infer' + } + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = Channel.of([ + [id: 'fasta'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ]) + input[2] = ULTRA_INDEX.out.pickle + .join(ULTRA_INDEX.out.database) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + sanitizeOutput(process.out, unstableKeys: ["bam"]) + ).match() } + ) + } + } + + test("ultra_align -- stub") { + options "-stub" + when { + params { + gnu_sort_args = '' + ultra_index_args = '' + } + process { + """ + input[0] = [[id: 'test'], []] + input[1] = [ + [id: 'fasta'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true), + ] + input[2] = [[id: 'index'], [], []] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + sanitizeOutput(process.out) + ).match() } + ) + } + } +} diff --git a/modules/nf-core/ultra/align/tests/main.nf.test.snap b/modules/nf-core/ultra/align/tests/main.nf.test.snap new file mode 100644 index 0000000..bccd5b9 --- /dev/null +++ b/modules/nf-core/ultra/align/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "ultra_align -- stub": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_samtools": [ + [ + "ULTRA_ALIGN", + "samtools", + "1.17" + ] + ], + "versions_ultra": [ + [ + "ULTRA_ALIGN", + "ultra", + "0.1" + ] + ] + } + ], + "timestamp": "2026-06-18T07:45:00.39092562", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "ultra_align": { + "content": [ + "4a12eec345cffd63b51bd3d29d89f13c", + { + "bam": [ + [ + { + "id": "test" + }, + "test.bam" + ] + ], + "versions_samtools": [ + [ + "ULTRA_ALIGN", + "samtools", + "1.17" + ] + ], + "versions_ultra": [ + [ + "ULTRA_ALIGN", + "ultra", + "0.1" + ] + ] + } + ], + "timestamp": "2026-06-18T08:42:51.310969523", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/ultra/align/tests/nextflow.config b/modules/nf-core/ultra/align/tests/nextflow.config new file mode 100644 index 0000000..95a26a0 --- /dev/null +++ b/modules/nf-core/ultra/align/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: "GNU_SORT" { + ext.args = params.gnu_sort_args + } + + withName: "ULTRA_INDEX" { + ext.args = params.ultra_index_args + } +} diff --git a/modules/nf-core/ultra/index/environment.yml b/modules/nf-core/ultra/index/environment.yml index 81f92d0..4098444 100644 --- a/modules/nf-core/ultra/index/environment.yml +++ b/modules/nf-core/ultra/index/environment.yml @@ -1,7 +1,10 @@ -name: ultra_index channels: - conda-forge - bioconda - - defaults + dependencies: + - bioconda::gffutils=0.11.1 + - bioconda::samtools=1.17 - bioconda::ultra_bioinformatics=0.1 + - conda-forge::python=3.10.12 + - conda-forge::sqlite=3.42.0 diff --git a/modules/nf-core/ultra/index/main.nf b/modules/nf-core/ultra/index/main.nf index 29d3b53..e2a1cce 100644 --- a/modules/nf-core/ultra/index/main.nf +++ b/modules/nf-core/ultra/index/main.nf @@ -1,37 +1,59 @@ process ULTRA_INDEX { - tag "$gtf" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.1--pyh7cba7a3_1': - 'biocontainers/ultra_bioinformatics:0.1--pyh7cba7a3_1' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:c2c0cd48e7ed1cf3f365b421c7389d04e6bfa812-0': + 'quay.io/biocontainers/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:c2c0cd48e7ed1cf3f365b421c7389d04e6bfa812-0' }" input: - path fasta - path gtf + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) output: - tuple path("*.pickle"), path("*.db"), emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("*.db"), emit: database + tuple val(meta), path("*.pickle"), emit: pickle + tuple val("${task.process}"), val('ultra'), eval("uLTRA --version | sed 's/uLTRA //'"), emit: versions_ultra, topic: versions + tuple val("${task.process}"), val('gffutils'), eval("python -c 'import gffutils; print(gffutils.__version__)'"), emit: versions_gffutils, topic: versions + tuple val("${task.process}"), val('sqlite'), eval("python -c 'import sqlite3; print(sqlite3.sqlite_version)'"), emit: versions_sqlite, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${gtf.baseName}" + def args = task.ext.args ?: '' """ uLTRA \\ index \\ - $args \\ - $fasta \\ - $gtf \\ + ${args} \\ + ${fasta} \\ + ${gtf} \\ ./ + """ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ultra: \$( uLTRA --version|sed 's/uLTRA //g' ) - END_VERSIONS + stub: + """ + touch database.db + touch all_splice_pairs_annotations.pickle + touch all_splice_sites_annotations.pickle + touch chr_to_id.pickle + touch exon_choordinates_to_id.pickle + touch flank_choordinates.pickle + touch gene_to_small_segments.pickle + touch id_to_chr.pickle + touch max_intron_chr.pickle + touch parts_to_segments.pickle + touch ref_exon_sequences.pickle + touch ref_flank_sequences.pickle + touch ref_part_sequences.pickle + touch ref_segment_sequences.pickle + touch refs_id_lengths.pickle + touch refs_lengths.pickle + touch segment_id_to_choordinates.pickle + touch segment_to_gene.pickle + touch segment_to_ref.pickle + touch splices_to_transcripts.pickle + touch transcripts_to_splices.pickle """ } diff --git a/modules/nf-core/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml index 3c0eda9..771d16a 100644 --- a/modules/nf-core/ultra/index/meta.yml +++ b/modules/nf-core/ultra/index/meta.yml @@ -1,5 +1,6 @@ name: "ultra_index" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment +description: uLTRA aligner - A wrapper around minimap2 to improve small exon + detection - Index gtf file for reads alignment keywords: - uLTRA - index @@ -14,29 +15,113 @@ tools: documentation: "https://github.com/ksahlin/uLTRA" tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" - licence: "['GNU GPLV3']" + licence: + - "GNU GPLV3" + identifier: "" input: - - fasta: - type: file - description: A fasta file of the genome to use as reference for mapping - pattern: "*.{fasta, fa}" - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test' ] + - fasta: + type: file + description: A fasta file of the genome to use as reference for mapping + pattern: "*.{fasta, fa}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing gtf information + e.g. [ id:'test' ] + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + ontologies: [] output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pickle: - type: file - description: Index files generated by uLTRA index - pattern: "*.pickle" - - pickle: - type: file - description: database file generated by uLTRA index - pattern: "*.db" + database: + - - meta: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test' ] + - "*.db": + type: file + description: Index database + pattern: "*.db" + ontologies: [] + pickle: + - - meta: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test' ] + - "*.pickle": + type: file + description: Index file + pattern: "*.pickle" + ontologies: + - edam: http://edamontology.org/format_4002 + versions_ultra: + - - ${task.process}: + type: string + description: The name of the process + - ultra: + type: string + description: The name of the tool + - uLTRA --version | sed 's/uLTRA //': + type: eval + description: The expression to obtain the version of the tool + versions_gffutils: + - - ${task.process}: + type: string + description: The name of the process + - gffutils: + type: string + description: The name of the tool + - python -c 'import gffutils; print(gffutils.__version__)': + type: eval + description: The expression to obtain the version of the tool + versions_sqlite: + - - ${task.process}: + type: string + description: The name of the process + - sqlite: + type: string + description: The name of the tool + - python -c 'import sqlite3; print(sqlite3.sqlite_version)': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - ultra: + type: string + description: The name of the tool + - uLTRA --version | sed 's/uLTRA //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - gffutils: + type: string + description: The name of the tool + - python -c 'import gffutils; print(gffutils.__version__)': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - sqlite: + type: string + description: The name of the tool + - python -c 'import sqlite3; print(sqlite3.sqlite_version)': + type: eval + description: The expression to obtain the version of the tool authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/index/tests/main.nf.test b/modules/nf-core/ultra/index/tests/main.nf.test new file mode 100644 index 0000000..c8154cb --- /dev/null +++ b/modules/nf-core/ultra/index/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process ULTRA_INDEX" + config "./nextflow.config" + script "../main.nf" + process "ULTRA_INDEX" + + tag "modules" + tag "modules_nfcore" + tag "ultra" + tag "ultra/index" + tag "gnu" + tag "gnu/sort" + + test("ultra_index") { + setup { + run("GNU_SORT") { + script "../../../gnu/sort/main.nf" + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true), + "gtf" + ] + """ + } + } + } + when { + params { + gnu_sort_args = '-k1,1 -k4,4n' + ultra_index_args = '--disable_infer' + } + process { + """ + input[0] = [ + [id: "test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[1] = GNU_SORT.out.sorted + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + sanitizeOutput(process.out, unstableKeys: ["pickle"]) + ).match() } + ) + } + } + + test("ultra_index -- stub") { + options "-stub" + when { + params { + gnu_sort_args = '' + ultra_index_args = '' + } + process { + """ + input[0] = [ + [id: "test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[1] = [[], []] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + sanitizeOutput(process.out) + ).match() } + ) + } + } +} diff --git a/modules/nf-core/ultra/index/tests/main.nf.test.snap b/modules/nf-core/ultra/index/tests/main.nf.test.snap new file mode 100644 index 0000000..341c8f8 --- /dev/null +++ b/modules/nf-core/ultra/index/tests/main.nf.test.snap @@ -0,0 +1,140 @@ +{ + "ultra_index": { + "content": [ + { + "database": [ + [ + { + "id": "test" + }, + "database.db:md5,f9b780bf5a0a5d23256afb99df7137d9" + ] + ], + "pickle": [ + [ + { + "id": "test" + }, + [ + "all_splice_pairs_annotations.pickle", + "all_splice_sites_annotations.pickle", + "chr_to_id.pickle", + "exon_choordinates_to_id.pickle", + "flank_choordinates.pickle", + "gene_to_small_segments.pickle", + "id_to_chr.pickle", + "max_intron_chr.pickle", + "parts_to_segments.pickle", + "ref_exon_sequences.pickle", + "ref_flank_sequences.pickle", + "ref_part_sequences.pickle", + "ref_segment_sequences.pickle", + "refs_id_lengths.pickle", + "refs_lengths.pickle", + "segment_id_to_choordinates.pickle", + "segment_to_gene.pickle", + "segment_to_ref.pickle", + "splices_to_transcripts.pickle", + "transcripts_to_splices.pickle" + ] + ] + ], + "versions_gffutils": [ + [ + "ULTRA_INDEX", + "gffutils", + "0.11.1" + ] + ], + "versions_sqlite": [ + [ + "ULTRA_INDEX", + "sqlite", + "3.42.0" + ] + ], + "versions_ultra": [ + [ + "ULTRA_INDEX", + "ultra", + "0.1" + ] + ] + } + ], + "timestamp": "2026-06-18T08:17:40.761154394", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + }, + "ultra_index -- stub": { + "content": [ + { + "database": [ + [ + { + "id": "test" + }, + "database.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pickle": [ + [ + { + "id": "test" + }, + [ + "all_splice_pairs_annotations.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "all_splice_sites_annotations.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "chr_to_id.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "exon_choordinates_to_id.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "flank_choordinates.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "gene_to_small_segments.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "id_to_chr.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "max_intron_chr.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "parts_to_segments.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "ref_exon_sequences.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "ref_flank_sequences.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "ref_part_sequences.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "ref_segment_sequences.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "refs_id_lengths.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "refs_lengths.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "segment_id_to_choordinates.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "segment_to_gene.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "segment_to_ref.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "splices_to_transcripts.pickle:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcripts_to_splices.pickle:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_gffutils": [ + [ + "ULTRA_INDEX", + "gffutils", + "0.11.1" + ] + ], + "versions_sqlite": [ + [ + "ULTRA_INDEX", + "sqlite", + "3.42.0" + ] + ], + "versions_ultra": [ + [ + "ULTRA_INDEX", + "ultra", + "0.1" + ] + ] + } + ], + "timestamp": "2026-06-18T07:45:15.943436768", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/ultra/index/tests/nextflow.config b/modules/nf-core/ultra/index/tests/nextflow.config new file mode 100644 index 0000000..c37ac08 --- /dev/null +++ b/modules/nf-core/ultra/index/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: "GNU_SORT" { + ext.args = params.gnu_sort_args + ext.prefix = { "${meta.id}_sorted" } + } + + withName: "ULTRA_INDEX" { + ext.args = params.ultra_index_args + } +} diff --git a/nextflow.config b/nextflow.config index 3f348ca..4619aa2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,7 +13,8 @@ params { input = null primers = null rq = 0.9 - chunk = 40 + chunk_ccs = 40 + chunk_mapping = 100 capped = false five_prime = 100 splice_junction = 10 @@ -24,8 +25,7 @@ params { top_passes = 60 min_length = 10 max_length = 50000 - entrypoint = "isoseq" - + tama_merge_all = false // References genome = null @@ -46,50 +46,42 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = null help = false + help_full = false + show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/isoseq/' + trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true + validate_params = true +} +// Max resources +process { + resourceLimits = [ + cpus: 16, + memory: '128.GB', + time: '240.h' + ] } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/isoseq custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/isoseq.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/isoseq profiles: ${params.custom_config_base}/pipeline/isoseq.config") -} profiles { debug { dumpHashes = true @@ -127,7 +119,18 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { + arm64 { + process.arch = 'arm64' + // TODO https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { @@ -184,38 +187,49 @@ profiles { wave.freeze = true wave.strategy = 'conda,container' } - gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - test_minimap2 { includeConfig 'conf/test_minimap2.config' } - test_minimap2_map_entrypoint { includeConfig 'conf/test_minimap2_map_entrypoint.config' } - test_ultra_map_entrypoint { includeConfig 'conf/test_ultra_map_entrypoint.config' } + test { includeConfig 'conf/test.config' } + test_minimap2 { includeConfig 'conf/test_minimap2.config' } + test_full { includeConfig 'conf/test_full.config' } + test_inputs_map { includeConfig 'conf/test_samplesheet_v2_map.config' } + test_inputs_lima { includeConfig 'conf/test_samplesheet_v2_lima.config' } + test_inputs_refine { includeConfig 'conf/test_samplesheet_v2_refine.config' } + test_inputs_ccs { includeConfig 'conf/test_samplesheet_v2_ccs.config' } + test_inputs_ccs_lima_refine_map_mergeAll { includeConfig 'conf/test_samplesheet_v2_ccs_lima_refine_map_mergeAll.config' } + test_inputs_ccs_lima_refine_map { includeConfig 'conf/test_samplesheet_v2_ccs_lima_refine_map.config' } + test_inputs_ccs_map { includeConfig 'conf/test_samplesheet_v2_ccs_map.config' } + test_inputs_lima_refine_map { includeConfig 'conf/test_samplesheet_v2_lima_refine_map.config' } + test_inputs_refine_map { includeConfig 'conf/test_samplesheet_v2_refine_map.config' } + test_inputs_multi_lib { includeConfig 'conf/test_samplesheet_v2_multi_lib.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different institutions + +// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. +// Load nf-core/isoseq custom profiles from different institutions. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} + +// Load nf-core/isoseq custom profiles from different institutions. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/isoseq.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -227,74 +241,65 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { - enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + enabled = true + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" + overwrite = true } report { - enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + enabled = true + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" + overwrite = true } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/isoseq' - author = """Sébastien Guizard (@sguizard)""" + // NOTE: `contribution` must not be the last field. nf-core tools 4.0.3 normalises this + // map to JSON with a naive replace("]]", "}]"), which corrupts a trailing nested list. + contributors = [[ + name: 'Sébastien Guizard', + contribution: ['author', 'maintainer'], + github: 'sguizard', + orcid: '0000-0001-5116-4150' + ]] homePage = 'https://github.com/nf-core/isoseq' description = """Genes and transcripts annotation with Isoseq using uLTRA and TAMA""" mainScript = 'main.nf' - doi = '10.5281/zenodo.7116979' - nextflowVersion = '!>=23.04.0' - version = '2.0.0' + defaultBranch = 'master' + nextflowVersion = '!>=25.10.4' + version = '3.0.0' doi = '10.1093/bioinformatics/btad150' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } - } +validation { + defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs } +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index ac9ab39..2e757f2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,16 +1,16 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/isoseq/master/nextflow_schema.json", "title": "nf-core/isoseq pipeline parameters", "description": "Genes and transcripts annotation with Isoseq using uLTRA and TAMA", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "outdir", "primers"], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -41,19 +41,18 @@ "description": "Genome annotation file", "help_text": "Provide a GTF annotation file (sorted by sequence and start) if you set the `--aligner` option to `uLTRA`\nGziped files are accepted. " }, - "entrypoint": { - "type": "string", - "fa_icon": "fas fa-dungeon", - "description": "Run complete pipeline or TAMA only?", - "enum": ["isoseq", "map"], - "default": "isoseq", - "help_text": "If you don't have the subreads sequences, because of the provider or last PacBio sequencer or because you used Oxford Nanopore, you'll to run the pipeline from the mapping step to advantage of the TAMA processing. \nThis option allows you to change the entry point from subread (--entrypoint isoseq) processing to mapping (--entrypoint map). " - }, - "chunk": { + "chunk_ccs": { "type": "integer", "default": 40, - "description": "If entrypoint 'isoseq', ccs --chunk option, define the number of batches to run in parallel. If entrypoint 'map', split fasta in files of 'chunk' sequences.", - "help_text": "If selected entrypoint is 'isoseq' (default): \nCCS workload can be split into to chunks for a faster running time. \nThis value must be a positive integer greater than 1. \n```bash\n--chunk 1/10 \n```\n\nif selected entrypoint is 'map': the reads files will be split into files of 'chunk' sequences.", + "description": "Defines the number of batches to run in parallel for.", + "help_text": "CCS workload can be split into to chunks for a faster running time. \nThis value must be a positive integer greater than 1. \n```bash\n--chunk 1/10 \n```\n\n", + "fa_icon": "fas fa-cog" + }, + "chunk_mapping": { + "type": "integer", + "default": 100, + "description": "Splits fasta in files of 'chunk' sequences.", + "help_text": "The fasta files will be split into files of 'chunk' sequences.", "fa_icon": "fas fa-cog" }, "email": { @@ -170,6 +169,13 @@ "description": "TAMA collapse: 3 prime wobble threshold", "help_text": "Set the maximum threshold for collapsing 3 prime exon.\n```\n--three_prime 100\n```", "fa_icon": "fas fa-cog" + }, + "tama_merge_all": { + "type": "boolean", + "default": false, + "description": "TAMA merge: merge the sample-wise annotations into a single annotation?", + "help_text": "By default, the pipeline one anntation per sample. \nAdding this option will compute an addiontional annotation by merging all samples.", + "fa_icon": "fas fa-question-circle" } }, "fa_icon": "fas fa-cogs" @@ -202,6 +208,13 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -253,41 +266,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -295,12 +273,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -344,13 +316,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", @@ -376,61 +341,55 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/isoseq/", "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", + "hidden": true + }, + "help": { + "type": ["boolean", "string"], + "description": "Display the help message." + }, + "help_full": { + "type": "boolean", + "description": "Display the full detailed help message." + }, + "show_hidden": { + "type": "boolean", + "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." } } } }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/ccs_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/aligner_option" + "$ref": "#/$defs/ccs_options" }, { - "$ref": "#/definitions/tama_options" + "$ref": "#/$defs/aligner_option" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/tama_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..9ba7e6d --- /dev/null +++ b/nf-test.config @@ -0,0 +1,38 @@ +config { + // location for all nf-test tests + testsDir = "." + + // nf-test directory including temporary files for each test + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" + + // location of an optional nextflow.config file specific for executing tests + configFile = "tests/nextflow.config" + + // ignore tests coming from the nf-core/modules repo + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] + + // run all test with defined profile(s) from the main nextflow.config + profile = "test" + + // list of filenames or patterns that should be trigger a full test run + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] + + // load the necessary plugins + plugins { + load "nft-utils@0.0.7" + } +} diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 0000000..138d465 --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,341 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "Stable", + "datePublished": "2026-08-14T08:04:34+00:00", + "description": "

\n \n \n \"nf-core/isoseq\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/isoseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/isoseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/isoseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/isoseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/isoseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13694618-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13694618)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7116979-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7116979)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/isoseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23isoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/isoseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/isoseq** is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Starting from raw isoseq subreads, the pipeline:\n\n- Generates the Circular Consensus Sequences (CCS)\n\n- Clean and polish CCS to create Full Length Non Chimeric (FLNC) reads\n\n- Maps FLNCs on the genome\n\n- Define and clean gene models\n\n![isoseq_pipeline_graph](docs/images/Isoseq_pipeline_metro.png)\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/isoseq/results).\n\n## Pipeline summary\n\n1. Generate CCS consensuses from raw isoseq subreads (Optional, [`PBCCS`](https://github.com/PacificBiosciences/ccs))\n2. Remove primer sequences from consensuses (Optional, [`LIMA`](https://github.com/pacificbiosciences/barcoding/))\n3. Detect and remove chimeric reads ([`ISOSEQ3 REFINE`](https://github.com/PacificBiosciences/IsoSeq))\n4. Convert bam file into fasta file ([`BAMTOOLS CONVERT`](https://github.com/pezmaster31/bamtools))\n5. Select reads with a polyA tail and trim it ([`GSTAMA_POLYACLEANUP`](https://github.com/GenomeRIK/tama))\n6. uLTRA path: decompress FLNCs ([`GUNZIP`](https://www.gnu.org/software/gzip/))\n7. uLTRA path: index `GTF` file for mapping ([`uLTRA`](https://github.com/ksahlin/ultra))\n8. Map consensuses on the reference genome ([`MINIMAP2`](https://github.com/lh3/minimap2) or [`uLTRA`](https://github.com/ksahlin/ultra))\n9. Clean gene models ([`TAMA collapse`](https://github.com/GenomeRIK/tama))\n10. Merge annotations by sample ([`TAMA merge`](https://github.com/GenomeRIK/tama))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,seq_data,pbi,start_from\nsample1,sample1.subreads.bam,sample1.subreads.bam.pbi,ccs\nsample2,sample2.ccs.bam,none,lima\nsample3,sample3.fl.primer_5p--primer_3p.bam,none,refine\nsample4,sample4.long_reads.fa.gz,none,mapping\n```\n\nThe file list all datasets to analyse. Those datasets can be raw subreads, Circular Consensus Sequences (CCS), Full Length sequences produced by LIMA (Pacbio software suite), or long reads sequence Pacbio Hifi (or Oxford Nanopore long reads!)\nThe first column define the sample ID, the second sequence data file, the third PacBio Index file (subreads only) and the program where to start the analysis.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/isoseq \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --genome \\\n --primers \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/isoseq/usage) and the [parameter documentation](https://nf-co.re/isoseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/isoseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/isoseq/output).\n\n## Credits\n\nnf-core/isoseq was originally written by S\u00e9bastien Guizard.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Thanks to [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa), [Daniel Schreyer](https://github.com/DSchreyer), [Gisela Gabernet](https://github.com/ggabernet) and [Maxime U Garcia](https://github.com/maxulysse) for their reviews and contributions\n- [Kristoffer Sahlin](https://github.com/ksahlin) for `uLTRA` and the help he provided\n- [Richard Kuo](https://github.com/GenomeRIK) ([Wobble Genomics](https://www.wobblegenomics.com/)) for his valuable advices on isoseq analysis\n- The Workpackage 2 of [GENE-SWitCH Project](https://www.gene-switch.eu/) for their fruitful discussions and remarks\n- [Mick Watson](https://twitter.com/BioMickWatson) group for their support\n- The nf-core community for their help in the development of this pipeline\n- [James A. Fellows Yates](https://github.com/jfy133) & nf-core for the metro map style components for pipeline graph\n- [J\u00falia Mir Pedrol](https://github.com/mirpedrol) for debugging help\n- [Usman Rashid](https://github.com/GallVp) for his contributions on pipeline development\n\nThis pipeline has been developed as part of the GENE-SWitCH project. This project has received funding from the European Union's Horizon 2020 Research and Innovation Programme under the grant agreement n\u00b0 817998.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#isoseq` channel](https://nfcore.slack.com/channels/isoseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nYou can cite the `nf-core/isoseq` publication as follows:\n\n> **nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing**\n>\n> S\u00e9bastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard I Kuo, Megan Davey, Alan Archibald & Mick Watson.\n>\n> Bioinformatics, Volume 39, Issue 5, May 2023. doi: [10.1093/bioinformatics/btad150](https://doi.org/10.1093/bioinformatics/btad150)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/local/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/isoseq", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#d725db7e-1687-40b9-bd18-e2fba8d19874" + } + ], + "name": "nf-core/isoseq" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], + "author": [ + { + "@id": "https://orcid.org/0000-0001-5116-4150" + } + ], + "dateCreated": "", + "dateModified": "2026-08-11T15:55:23Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": [ + "nf-core", + "nextflow", + "isoseq", + "isoseq-3", + "rna", + "tama", + "ultra" + ], + "license": [ + "MIT" + ], + "maintainer": [ + { + "@id": "https://orcid.org/0000-0001-5116-4150" + } + ], + "name": [ + "nf-core/isoseq" + ], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": [ + "https://github.com/nf-core/isoseq", + "https://nf-co.re/isoseq/3.0.0/" + ], + "version": [ + "3.0.0" + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=25.10.4" + }, + { + "@id": "#d725db7e-1687-40b9-bd18-e2fba8d19874", + "@type": "TestSuite", + "instance": [ + { + "@id": "#4acf8098-a0b6-448e-9865-b02e1488f578" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for nf-core/isoseq" + }, + { + "@id": "#4acf8098-a0b6-448e-9865-b02e1488f578", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing nf-core/isoseq", + "resource": "repos/nf-core/isoseq/actions/workflows/nf-test.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CODE_OF_CONDUCT.md", + "@type": "File", + "description": "The nf-core code of conduct" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + }, + { + "@id": "https://orcid.org/0000-0001-5116-4150", + "@type": "Person", + "email": "sguizard@ed.ac.uk", + "name": "S\u00e9bastien Guizard", + "url": "https://github.com/sguizard" + } + ] +} \ No newline at end of file diff --git a/subworkflows/local/chunker/main.nf b/subworkflows/local/chunker/main.nf new file mode 100644 index 0000000..8cffdac --- /dev/null +++ b/subworkflows/local/chunker/main.nf @@ -0,0 +1,43 @@ +// +// Takes fasta from LIMA and ISOSEQ REFINE inputs and splits their generated fastas +// + +workflow CHUNKER { + take: + ch_input_fastas // Channel: [ meta[id, start_from ], fasta ] + chunk // value: integer (number of chunk to create) + in_decompress // value: true or false + out_compress // value: true or false + + main: + // ch_input_fastas.view { meta, fa -> println("CHUNKER:ch_input_fastas: $meta | $fa") } + + ch_input_fastas + .branch { meta, _fasta -> + chunk : meta.id =~ /chunk/ + to_chunk: !(meta.id =~ /chunk/) + } + .set { ch_input_fastas_branched } + + // ch_input_fastas_branched.chunk.view { meta, fa -> println("CHUNKER:ch_input_fastas_branched.chunk: $meta | $fa") } + // ch_input_fastas_branched.to_chunk.view { meta, fa -> println("CHUNKER:ch_input_fastas_branched.to_chunk: $meta | $fa") } + + ch_input_fastas_branched.to_chunk + .splitFasta( + by: chunk, + decompress: in_decompress, + file: "chunk", + compress: out_compress + ) + .map { meta, file -> + def chk = (file =~ /(chunk\.\d+)(?:\.gz)?$/)[ 0 ][ 1 ] + def id_former = meta.id + def id_new = meta.id + "." + chk + [ [ id:id_new, id_former:id_former, start_from:meta.start_from ] , file ] + } + .concat(ch_input_fastas_branched.chunk) + .set { fastas } + + emit: + fastas +} diff --git a/subworkflows/local/set_chunk_num_channel.nf b/subworkflows/local/set_chunk_num_channel/main.nf similarity index 58% rename from subworkflows/local/set_chunk_num_channel.nf rename to subworkflows/local/set_chunk_num_channel/main.nf index fd69838..246e89b 100644 --- a/subworkflows/local/set_chunk_num_channel.nf +++ b/subworkflows/local/set_chunk_num_channel/main.nf @@ -8,14 +8,10 @@ workflow SET_CHUNK_NUM_CHANNEL { chunk // value: integer (number of chunk to create) main: - int n_samples = -1 + int n_samples = file(samplesheet).readLines().size() - 1 - file(samplesheet) - .readLines() - .each { n_samples++ } - - Channel // Prepare the pbccs chunk_num channel - .from((1..chunk).step(1).toList()*n_samples) + channel // Prepare the pbccs chunk_num channel + .from((1..(chunk as int)).step(1).toList()*n_samples) .set { chunk_num } emit: diff --git a/subworkflows/local/set_value_channel.nf b/subworkflows/local/set_value_channel/main.nf similarity index 80% rename from subworkflows/local/set_value_channel.nf rename to subworkflows/local/set_value_channel/main.nf index e82778d..f36698b 100644 --- a/subworkflows/local/set_value_channel.nf +++ b/subworkflows/local/set_value_channel/main.nf @@ -2,7 +2,7 @@ // Check input samplesheet and get read channels // -include { GUNZIP } from '../../modules/nf-core/gunzip/main' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main' workflow SET_VALUE_CHANNEL { take: @@ -16,7 +16,7 @@ workflow SET_VALUE_CHANNEL { .set { data } } else { - Channel // Prepare value channel + channel // Prepare value channel .value(file(infile)) .set { data } } diff --git a/subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf index 763a11b..4eecf64 100644 --- a/subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf @@ -8,38 +8,37 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + help // boolean: Display help message and exit + help_full // boolean: Show the full help message + show_hidden // boolean: Show hidden parameters in the help message main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Print version and exit if required and dump pipeline parameters to JSON file @@ -54,16 +53,43 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + + def before_text = "" + def after_text = "" + before_text = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m nf-core/isoseq ${workflow.manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> " https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/isoseq/blob/master/CITATIONS.md +""" + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null, + help, + help_full, + show_hidden, + before_text, + after_text, + command, + false ) // @@ -72,6 +98,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -80,41 +107,35 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - if (params.entrypoint == "isoseq") { - Channel - .fromSamplesheet("input") - .flatMap { create_pbccs_channel(it, params.chunk) } - .set { ch_samplesheet } - } + def samplesheet_rows = samplesheetToList(params.input, "${projectDir}/assets/schema_input.json") - if (params.entrypoint == "map") { - Channel - .fromSamplesheet("input") - .flatMap { create_reads_channel(it) } - .splitFasta( - by: params.chunk, - decompress: true, - file: "chunk", - compress: true - ) - .map { - def chk = (it[1] =~ /(chunk\.\d+)\.gz/)[ 0 ][ 1 ] - def id_former = it[0].id - def id_new = it[0].id + "." + chk - [ [ id:id_new, id_former:id_former ] , it[1] ] - } - .set { ch_samplesheet } + // Primers are consumed only by LIMA and ISOSEQ_REFINE + def needs_primers = samplesheet_rows.any { row -> row[0].start_from in ['ccs', 'lima', 'refine'] } + + if (needs_primers && !params.primers) { + error( + "Missing required parameter --primers.\n" + + "A primer FASTA is required when any sample starts from 'ccs', 'lima' or 'refine'.\n" + + "It is optional only when every sample uses start_from: 'mapping'.") } + channel + .fromList(samplesheet_rows.withIndex()) + .flatMap { pair -> + def row = pair[0] + def counter = pair[1] as int + create_samplesheet_channel(row, params.chunk_ccs, counter) } + .set { ch_samplesheet } + emit: samplesheet = ch_samplesheet versions = ch_versions } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -125,43 +146,50 @@ workflow PIPELINE_COMPLETION { plaintext_email // boolean: Send plain-text email instead of HTML outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def multiqc_reports = multiqc_report.toList() // // Completion email and summary // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_reports.getVal(), + ) } completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } } workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters // def validateInputParameters() { genomeExistsError() + if (!params.fasta) { + error("Missing genome. \nA genome to annotate must be provided with the --fasta or --genome option.\n") + } } // @@ -171,7 +199,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -203,18 +231,21 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", + "CCS (PacBio),", + "Lima (PacBio),", + "IsoSeq (PacBio),", + "SAMtools (Danecek et al. 2021),", + "uLTRA (Sahlin and Mäkinen 2021),", + "minimap2 (Li 2018),", + "BamTools (Barnett et al. 2011),", + "TAMA (Kuo et al. 2020),", + "MultiQC (Ewels et al. 2016),", "." ].join(' ').trim() @@ -222,19 +253,23 @@ def toolCitationText() { } def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + '
  • PacBio. CCS: Generate highly accurate single-molecule consensus reads. URL: https://ccs.how/
    • ', + '
  • PacBio. Lima: Demultiplex barcoded PacBio data. URL: https://lima.how/
    • ', + '
  • PacBio. IsoSeq: Characterisation of full-length transcripts. URL: https://github.com/PacificBiosciences/IsoSeq
    • ', + '
  • Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. doi: 10.1093/gigascience/giab008
    • ', + '
  • Sahlin, K., & Mäkinen, V. (2021). Accurate spliced alignment of long RNA sequencing reads. Bioinformatics, btab540. doi: 10.1093/bioinformatics/btab540
    • ', + '
  • Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100. doi: 10.1093/bioinformatics/bty191
    • ', + '
  • Barnett, D. W., Garrison, E. K., Quinlan, A. R., Strömberg, M. P., & Marth, G. T. (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691-1692. doi: 10.1093/bioinformatics/btr174
    • ', + '
  • Kuo, R. I., Cheng, Y., Zhang, R., et al. (2020). Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics, 21, 751. doi: 10.1186/s12864-020-07123-7
    • ', + '
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. doi: 10.1093/bioinformatics/btw354
    • ' ].join(' ').trim() return reference_text } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() @@ -245,20 +280,17 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - // meta["tool_bibliography"] = toolBibliographyText() - + meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_bibliography"] = toolBibliographyText() def methods_text = mqc_methods_yaml.text @@ -268,30 +300,54 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } -// Function to get to create samplesheet channel for isoseq entrypoint [ meta, bam, pbi ] -def create_pbccs_channel(row, chunk) { - +// Function to get samplesheet channel from samplesheet version 2 +def create_samplesheet_channel(row, chunk, counter) { + // Check if mandatory seq_data file exists if (!file(row[1]).exists()) { - exit 1, "ERROR: Please check input samplesheet -> BAM file does not exist!\n${row[1]}" + error("Please check input samplesheet -> BAM file does not exist!\n${row[1]}") } - if (!file(row[2]).exists()) { - exit 1, "ERROR: Please check input samplesheet -> PBI file does not exist!\n${row[2]}" - } - - def array = [] - for ( i = 1 ; i <= chunk ; i++ ) { - array << [ row[0], file(row[1]), file(row[2]) ] - } + // returns depends on the starting point + if ( row[0].start_from == 'ccs' ) { // pbccs can work on chunks, need to as many entries as defined chunks + if (!file(row[2]).exists()) { + error("Please check input samplesheet -> PBI file does not exist!\n${row[2]}") + } - return array -} + return (1..chunk) + .collect { + [ + [ + id:row[0].id + "_" + counter, + start_from:row[0].start_from + ], + file(row[1]), + file(row[2]) + ] + } -// Function to get to create samplesheet channel for map entrypoint [ meta, reads ] -def create_reads_channel(row) { - if (!file(row[3]).exists()) { - exit 1, "ERROR: Please check input samplesheet -> reads file does not exist!\n${row[3]}" } - - return [ [ row[0], file(row[3]) ] ] + else if ( row[0].start_from in ['lima', 'refine']) { + return [ [ + [ + id:row[0].id + "_" + counter, + start_from:row[0].start_from + ], + file(row[1]), + null + ] ] + } + else if ( row[0].start_from == 'mapping') { + return [ [ + [ + id:row[0].id + "_" + counter, + start_from:row[0].start_from, + single_end:true + ], + file(row[1]), + null + ] ] + } + else { + error("Please check input samplesheet -> start_from value should be either: ccs, lima, refine, or mapping. (${row[0].start_from})") + } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28..d6e593e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,37 +85,42 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce..02dbf09 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926b..a09572e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f847611..0000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c3..afca543 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -21,27 +17,24 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,39 +45,22 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +78,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -113,8 +89,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -122,11 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // @@ -134,61 +106,40 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -200,79 +151,76 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - return mqc_report } // @@ -281,26 +229,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -317,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -337,40 +294,45 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -378,69 +340,16 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } -} - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f..f117040 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232..02c6701 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test new file mode 100644 index 0000000..8940d32 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap new file mode 100644 index 0000000..859d103 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c..0000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000..9ff0681 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,77 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + help // boolean: show help message + help_full // boolean: show full help message + show_hidden // boolean: show hidden parameters in help message + before_text // string: text to show before the help message and parameters summary + after_text // string: text to show after the help message and parameters summary + command // string: an example command of the pipeline + cli_typecast // boolean: whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour + + main: + + if(help || help_full) { + help_options = [ + beforeText: before_text, + afterText: after_text, + command: command, + showHidden: show_hidden, + fullHelp: help_full, + ] + if(parameters_schema) { + help_options << [parameters_schema: parameters_schema] + } + log.info paramsHelp( + help_options, + (help instanceof String && help != "true") ? help : "", + ) + exit 0 + } + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + + summary_options = [:] + if(parameters_schema) { + summary_options << [parameters_schema: parameters_schema] + } + log.info before_text + log.info paramsSummaryLog(summary_options, input_workflow) + log.info after_text + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + validateOptions = [:] + if(parameters_schema) { + validateOptions << [parameters_schema: parameters_schema] + } + if(cli_typecast != null) { + validateOptions << [cast_cli_params: cli_typecast] + } + validateParameters(validateOptions) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000..1d8c75a --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,59 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. + - help: + type: boolean, string + description: | + Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message. + - help_full: + type: boolean + description: Show the full help message and exit. + - show_hidden: + type: boolean + description: Show hidden parameters in the help message. + - before_text: + type: string + description: Text to show before the parameters summary and help message. + - after_text: + type: string + description: Text to show after the parameters summary and help message. + - command: + type: string + description: An example command to run the pipeline, to show in the help message and the summary. + - cli_typecast: + type: boolean + description: | + Whether to apply typecasting to the parameters given via the CLI before validation. + Set this to `null` to use the default behavior. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 0000000..1fd1eac --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,178 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should create a help message") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = true + input[4] = false + input[5] = false + input[6] = "Before" + input[7] = "After" + input[8] = "nextflow run test/test" + input[9] = null + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000..fd71cb8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.7.2" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c..331e0d2 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b0..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cff..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 0000000..61928f1 --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,24 @@ +.DS_Store +multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt +multiqc/multiqc_data/multiqc.parquet +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/llms-full.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html +fastqc/*_fastqc.{html,zip} +pipeline_info/*.{html,json,txt,yml} +**/*pickle +**/*.metrics.json.gz +**/*.report.json +**/*_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml +**/*_flnc.json +**/*_flnc.consensusreadset.xml +**/*consensusreadset.xml +**/*filter_summary.report.json +**/lima-filter-graph.txt +**/multiqc_ccs_report.txt +**/*.bam +**/*.bam.bai diff --git a/tests/default.nf.test b/tests/default.nf.test new file mode 100644 index 0000000..7afd259 --- /dev/null +++ b/tests/default.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test" + + test("-profile test") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assert workflow.success + assertAll( + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_path, + // All files with stable contents + stable_content + ).match() } + ) + } + } +} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..2d3cbdc --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,441 @@ +{ + "-profile test": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GNU_SORT": { + "coreutils": 9.5 + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "GUNZIP": { + "gunzip": 1.13 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "PBCCS": { + "pbccs": "6.4.0" + }, + "ULTRA_ALIGN": { + "samtools": 1.17, + "ultra": 0.1 + }, + "ULTRA_INDEX": { + "gffutils": "0.11.1", + "sqlite": "3.42.0", + "ultra": 0.1 + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + "01_PBCCS/sample1_0.chunk1.metrics.json.gz", + "01_PBCCS/sample1_0.chunk1.report.json", + "01_PBCCS/sample1_0.chunk1.report.txt", + "01_PBCCS/sample1_0.chunk2.bam", + "01_PBCCS/sample1_0.chunk2.bam.pbi", + "01_PBCCS/sample1_0.chunk2.metrics.json.gz", + "01_PBCCS/sample1_0.chunk2.report.json", + "01_PBCCS/sample1_0.chunk2.report.txt", + "01_PBCCS/sample1_0.chunk3.bam", + "01_PBCCS/sample1_0.chunk3.bam.pbi", + "01_PBCCS/sample1_0.chunk3.metrics.json.gz", + "01_PBCCS/sample1_0.chunk3.report.json", + "01_PBCCS/sample1_0.chunk3.report.txt", + "01_PBCCS/sample1_0.chunk4.bam", + "01_PBCCS/sample1_0.chunk4.bam.pbi", + "01_PBCCS/sample1_0.chunk4.metrics.json.gz", + "01_PBCCS/sample1_0.chunk4.report.json", + "01_PBCCS/sample1_0.chunk4.report.txt", + "01_PBCCS/sample1_0.chunk5.bam", + "01_PBCCS/sample1_0.chunk5.bam.pbi", + "01_PBCCS/sample1_0.chunk5.metrics.json.gz", + "01_PBCCS/sample1_0.chunk5.report.json", + "01_PBCCS/sample1_0.chunk5.report.txt", + "02_LIMA", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk1_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk1_flnc.json", + "02_LIMA/sample1_0.chunk1_flnc.lima.clips", + "02_LIMA/sample1_0.chunk1_flnc.lima.counts", + "02_LIMA/sample1_0.chunk1_flnc.lima.guess", + "02_LIMA/sample1_0.chunk1_flnc.lima.report", + "02_LIMA/sample1_0.chunk1_flnc.lima.summary", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk2_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk2_flnc.json", + "02_LIMA/sample1_0.chunk2_flnc.lima.clips", + "02_LIMA/sample1_0.chunk2_flnc.lima.counts", + "02_LIMA/sample1_0.chunk2_flnc.lima.guess", + "02_LIMA/sample1_0.chunk2_flnc.lima.report", + "02_LIMA/sample1_0.chunk2_flnc.lima.summary", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk3_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk3_flnc.json", + "02_LIMA/sample1_0.chunk3_flnc.lima.clips", + "02_LIMA/sample1_0.chunk3_flnc.lima.counts", + "02_LIMA/sample1_0.chunk3_flnc.lima.guess", + "02_LIMA/sample1_0.chunk3_flnc.lima.report", + "02_LIMA/sample1_0.chunk3_flnc.lima.summary", + "02_LIMA/sample1_0.chunk4_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk4_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk4_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk4_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk4_flnc.json", + "02_LIMA/sample1_0.chunk4_flnc.lima.clips", + "02_LIMA/sample1_0.chunk4_flnc.lima.counts", + "02_LIMA/sample1_0.chunk4_flnc.lima.guess", + "02_LIMA/sample1_0.chunk4_flnc.lima.report", + "02_LIMA/sample1_0.chunk4_flnc.lima.summary", + "02_LIMA/sample1_0.chunk5_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk5_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk5_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk5_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk5_flnc.json", + "02_LIMA/sample1_0.chunk5_flnc.lima.clips", + "02_LIMA/sample1_0.chunk5_flnc.lima.counts", + "02_LIMA/sample1_0.chunk5_flnc.lima.guess", + "02_LIMA/sample1_0.chunk5_flnc.lima.report", + "02_LIMA/sample1_0.chunk5_flnc.lima.summary", + "03_ISOSEQ_REFINE", + "03_ISOSEQ_REFINE/sample1_0.chunk1.bam", + "03_ISOSEQ_REFINE/sample1_0.chunk1.bam.pbi", + 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\ No newline at end of file diff --git a/tests/inputs_ccs.nf.test b/tests/inputs_ccs.nf.test new file mode 100644 index 0000000..eaaa511 --- /dev/null +++ b/tests/inputs_ccs.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs ccs" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_ccs" + + test("-profile test_inputs_ccs") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_ccs.nf.test.snap b/tests/inputs_ccs.nf.test.snap new file mode 100644 index 0000000..17e36b1 --- /dev/null +++ b/tests/inputs_ccs.nf.test.snap @@ -0,0 +1,398 @@ +{ + "-profile test_inputs_ccs": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + }, + "PBCCS": { + "pbccs": "6.4.0" + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + 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stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_ccs_lima_refine_map.nf.test.snap b/tests/inputs_ccs_lima_refine_map.nf.test.snap new file mode 100644 index 0000000..12b06db --- /dev/null +++ b/tests/inputs_ccs_lima_refine_map.nf.test.snap @@ -0,0 +1,664 @@ +{ + "-profile test_inputs_ccs_lima_refine_map": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + }, + "PBCCS": { + "pbccs": "6.4.0" + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + "01_PBCCS/sample1_0.chunk1.metrics.json.gz", + "01_PBCCS/sample1_0.chunk1.report.json", + "01_PBCCS/sample1_0.chunk1.report.txt", + "01_PBCCS/sample1_0.chunk2.bam", + "01_PBCCS/sample1_0.chunk2.bam.pbi", + "01_PBCCS/sample1_0.chunk2.metrics.json.gz", + "01_PBCCS/sample1_0.chunk2.report.json", + "01_PBCCS/sample1_0.chunk2.report.txt", + "01_PBCCS/sample1_0.chunk3.bam", + "01_PBCCS/sample1_0.chunk3.bam.pbi", + "01_PBCCS/sample1_0.chunk3.metrics.json.gz", + "01_PBCCS/sample1_0.chunk3.report.json", + "01_PBCCS/sample1_0.chunk3.report.txt", + "01_PBCCS/sample1_0.chunk4.bam", + "01_PBCCS/sample1_0.chunk4.bam.pbi", + "01_PBCCS/sample1_0.chunk4.metrics.json.gz", + "01_PBCCS/sample1_0.chunk4.report.json", + "01_PBCCS/sample1_0.chunk4.report.txt", + "01_PBCCS/sample1_0.chunk5.bam", + "01_PBCCS/sample1_0.chunk5.bam.pbi", + "01_PBCCS/sample1_0.chunk5.metrics.json.gz", + "01_PBCCS/sample1_0.chunk5.report.json", + "01_PBCCS/sample1_0.chunk5.report.txt", + "02_LIMA", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk1_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk1_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk1_flnc.json", + "02_LIMA/sample1_0.chunk1_flnc.lima.clips", + "02_LIMA/sample1_0.chunk1_flnc.lima.counts", + "02_LIMA/sample1_0.chunk1_flnc.lima.guess", + "02_LIMA/sample1_0.chunk1_flnc.lima.report", + "02_LIMA/sample1_0.chunk1_flnc.lima.summary", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk2_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk2_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk2_flnc.json", + "02_LIMA/sample1_0.chunk2_flnc.lima.clips", + "02_LIMA/sample1_0.chunk2_flnc.lima.counts", + "02_LIMA/sample1_0.chunk2_flnc.lima.guess", + "02_LIMA/sample1_0.chunk2_flnc.lima.report", + "02_LIMA/sample1_0.chunk2_flnc.lima.summary", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample1_0.chunk3_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample1_0.chunk3_flnc.consensusreadset.xml", + "02_LIMA/sample1_0.chunk3_flnc.json", + "02_LIMA/sample1_0.chunk3_flnc.lima.clips", + "02_LIMA/sample1_0.chunk3_flnc.lima.counts", + 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+ } + } +} \ No newline at end of file diff --git a/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test b/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test new file mode 100644 index 0000000..1c559bd --- /dev/null +++ b/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs ccs lima refine map and merge all samples" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_ccs_lima_refine_map_mergeAll" + + test("-profile test_inputs_ccs_lima_refine_map_mergeAll") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test.snap b/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test.snap new file mode 100644 index 0000000..be3c207 --- /dev/null +++ b/tests/inputs_ccs_lima_refine_map_mergeAll.nf.test.snap @@ -0,0 +1,677 @@ +{ + "-profile test_inputs_ccs_lima_refine_map_mergeAll": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_MERGE_ALL": { + "gstama": "0.0.1" + }, + 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"multiqc_general_stats.txt:md5,f60e94deef7b1d8f6f4c5e67b325e6ba", + "multiqc_lima_counts.txt:md5,d00757e4773f621db4f5459ca7a21088", + "multiqc_lima_summary.txt:md5,ab0445a6efcf301bc96362c62743c273" + ] + ], + "timestamp": "2026-08-14T15:04:51.339227064", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/inputs_ccs_map.nf.test b/tests/inputs_ccs_map.nf.test new file mode 100644 index 0000000..2326935 --- /dev/null +++ b/tests/inputs_ccs_map.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs ccs map" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_ccs_map" + + test("-profile test_inputs_ccs_map") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_ccs_map.nf.test.snap b/tests/inputs_ccs_map.nf.test.snap new file mode 100644 index 0000000..d6fcdf4 --- /dev/null +++ b/tests/inputs_ccs_map.nf.test.snap @@ -0,0 +1,508 @@ +{ + "-profile test_inputs_ccs_map": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + }, + "PBCCS": { + "pbccs": "6.4.0" + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + "01_PBCCS/sample1_0.chunk1.metrics.json.gz", + "01_PBCCS/sample1_0.chunk1.report.json", + "01_PBCCS/sample1_0.chunk1.report.txt", + "01_PBCCS/sample1_0.chunk2.bam", + "01_PBCCS/sample1_0.chunk2.bam.pbi", + "01_PBCCS/sample1_0.chunk2.metrics.json.gz", + "01_PBCCS/sample1_0.chunk2.report.json", + "01_PBCCS/sample1_0.chunk2.report.txt", + "01_PBCCS/sample1_0.chunk3.bam", + "01_PBCCS/sample1_0.chunk3.bam.pbi", + "01_PBCCS/sample1_0.chunk3.metrics.json.gz", + "01_PBCCS/sample1_0.chunk3.report.json", + "01_PBCCS/sample1_0.chunk3.report.txt", + "01_PBCCS/sample1_0.chunk4.bam", + "01_PBCCS/sample1_0.chunk4.bam.pbi", + 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100644 index 0000000..40c0431 --- /dev/null +++ b/tests/inputs_lima.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs lima" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_lima" + + test("-profile test_inputs_lima") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_lima.nf.test.snap b/tests/inputs_lima.nf.test.snap new file mode 100644 index 0000000..6e3cfab --- /dev/null +++ b/tests/inputs_lima.nf.test.snap @@ -0,0 +1,268 @@ +{ + "-profile test_inputs_lima": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + } + }, + [ + "02_LIMA", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample2_0_flnc.consensusreadset.xml", + "02_LIMA/sample2_0_flnc.json", + "02_LIMA/sample2_0_flnc.lima.clips", + "02_LIMA/sample2_0_flnc.lima.counts", + "02_LIMA/sample2_0_flnc.lima.guess", + "02_LIMA/sample2_0_flnc.lima.report", + "02_LIMA/sample2_0_flnc.lima.summary", + "03_ISOSEQ_REFINE", + "03_ISOSEQ_REFINE/sample2_0.bam", + "03_ISOSEQ_REFINE/sample2_0.bam.pbi", + "03_ISOSEQ_REFINE/sample2_0.consensusreadset.xml", + "03_ISOSEQ_REFINE/sample2_0.filter_summary.report.json", + "03_ISOSEQ_REFINE/sample2_0.report.csv", + "04_BAMTOOLS_CONVERT", + "04_BAMTOOLS_CONVERT/sample2_0.fasta", + "05_GSTAMA_POLYACLEANUP", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.5_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.5_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.5_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.6_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.6_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.6_tama_tails.fa.gz", + "06_MINIMAP2", + "06_MINIMAP2/sample2_0.chunk.1.bam", + "06_MINIMAP2/sample2_0.chunk.1.bam.bai", + "06_MINIMAP2/sample2_0.chunk.2.bam", + "06_MINIMAP2/sample2_0.chunk.2.bam.bai", + "06_MINIMAP2/sample2_0.chunk.3.bam", + "06_MINIMAP2/sample2_0.chunk.3.bam.bai", + "06_MINIMAP2/sample2_0.chunk.4.bam", + "06_MINIMAP2/sample2_0.chunk.4.bam.bai", + "06_MINIMAP2/sample2_0.chunk.5.bam", + "06_MINIMAP2/sample2_0.chunk.5.bam.bai", + "06_MINIMAP2/sample2_0.chunk.6.bam", + "06_MINIMAP2/sample2_0.chunk.6.bam.bai", + "07_GSTAMA_COLLAPSE", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.1_variants.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.2_variants.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.3_variants.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.4_variants.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.5_variants.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_polya.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_read.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_varcov.txt", + "07_GSTAMA_COLLAPSE/sample2_0.chunk.6_variants.txt", + "08_GSTAMA_FILELIST", + "08_GSTAMA_FILELIST/sample2.tsv", + "09_GSTAMA_MERGE", + "09_GSTAMA_MERGE/sample2.bed", + "09_GSTAMA_MERGE/sample2_gene_report.txt", + "09_GSTAMA_MERGE/sample2_merge.txt", + "09_GSTAMA_MERGE/sample2_trans_report.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/lima-filter-graph.txt", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_lima_counts.txt", + "multiqc/multiqc_data/multiqc_lima_summary.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/lima-filter-graph-cnt.pdf", + "multiqc/multiqc_plots/pdf/lima-filter-graph-pct.pdf", + "multiqc/multiqc_plots/pdf/multiqc_lima_counts.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/lima-filter-graph-cnt.png", + "multiqc/multiqc_plots/png/lima-filter-graph-pct.png", + "multiqc/multiqc_plots/png/multiqc_lima_counts.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/lima-filter-graph-cnt.svg", + "multiqc/multiqc_plots/svg/lima-filter-graph-pct.svg", + "multiqc/multiqc_plots/svg/multiqc_lima_counts.svg", 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newline at end of file diff --git a/tests/inputs_lima_refine_map.nf.test b/tests/inputs_lima_refine_map.nf.test new file mode 100644 index 0000000..d5aaf0e --- /dev/null +++ b/tests/inputs_lima_refine_map.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs lima refine map" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_lima_refine_map" + + test("-profile test_inputs_lima_refine_map") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_lima_refine_map.nf.test.snap b/tests/inputs_lima_refine_map.nf.test.snap new file mode 100644 index 0000000..a85918e --- /dev/null +++ b/tests/inputs_lima_refine_map.nf.test.snap @@ -0,0 +1,343 @@ +{ + "-profile test_inputs_lima_refine_map": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + } + }, + [ + "02_LIMA", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.bam", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.bam.pbi", + "02_LIMA/sample2_0_flnc.NEB_5p--NEB_Clontech_3p.consensusreadset.xml", + "02_LIMA/sample2_0_flnc.consensusreadset.xml", + "02_LIMA/sample2_0_flnc.json", + "02_LIMA/sample2_0_flnc.lima.clips", + "02_LIMA/sample2_0_flnc.lima.counts", + "02_LIMA/sample2_0_flnc.lima.guess", + "02_LIMA/sample2_0_flnc.lima.report", + "02_LIMA/sample2_0_flnc.lima.summary", + "03_ISOSEQ_REFINE", + "03_ISOSEQ_REFINE/sample2_0.bam", + "03_ISOSEQ_REFINE/sample2_0.bam.pbi", + "03_ISOSEQ_REFINE/sample2_0.consensusreadset.xml", + "03_ISOSEQ_REFINE/sample2_0.filter_summary.report.json", + "03_ISOSEQ_REFINE/sample2_0.report.csv", + "03_ISOSEQ_REFINE/sample3_1.bam", + "03_ISOSEQ_REFINE/sample3_1.bam.pbi", + "03_ISOSEQ_REFINE/sample3_1.consensusreadset.xml", + "03_ISOSEQ_REFINE/sample3_1.filter_summary.report.json", + "03_ISOSEQ_REFINE/sample3_1.report.csv", + "04_BAMTOOLS_CONVERT", + "04_BAMTOOLS_CONVERT/sample2_0.fasta", + "04_BAMTOOLS_CONVERT/sample3_1.fasta", + "05_GSTAMA_POLYACLEANUP", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.1_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.2_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.3_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.4_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample2_0.chunk.5_tama.fa.gz", + 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"sample2_0.chunk.5_read.txt:md5,f441d3c36963cc277178b4e1af275d1b", + "sample2_0.chunk.5_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample2_0.chunk.5_trans_read.bed:md5,8175932eec00949b37030106d9e84621", + "sample2_0.chunk.5_trans_report.txt:md5,178e21fb7ea02d1b84682dc2e934c330", + "sample2_0.chunk.5_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample2_0.chunk.5_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample2_0.chunk.6_collapsed.bed:md5,93c66ee57dbf302a6b2d99600cc730c4", + "sample2_0.chunk.6_local_density_error.txt:md5,0b62cde5a47f0a4dc2c0e4c26235b241", + "sample2_0.chunk.6_polya.txt:md5,2cb46eac9b00a08095b1bd4e0244559d", + "sample2_0.chunk.6_read.txt:md5,9ea2721f96d5efe63bc35850bbf12520", + "sample2_0.chunk.6_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample2_0.chunk.6_trans_read.bed:md5,2080114fac4005105ed4b8f291afd4b9", + "sample2_0.chunk.6_trans_report.txt:md5,15ad4aa7c425624464a179cf4d434e2e", + "sample2_0.chunk.6_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample2_0.chunk.6_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample3_1.chunk.1_collapsed.bed:md5,33f6bd7b72aa2957bbf0ceffc9ff1b32", + "sample3_1.chunk.1_local_density_error.txt:md5,25e666a9e8b3af9271532659a0b28013", + "sample3_1.chunk.1_polya.txt:md5,628ea62b918fc4f31e109f724d714a66", + "sample3_1.chunk.1_read.txt:md5,f5bedd14060f896f268d1aff22da3c5b", + "sample3_1.chunk.1_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample3_1.chunk.1_trans_read.bed:md5,86f4b69ae68a2ac46a38b9d82946f63e", + "sample3_1.chunk.1_trans_report.txt:md5,41739b80f8a4b828e8d91883c514166d", + "sample3_1.chunk.1_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample3_1.chunk.1_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4_2.chunk.1_collapsed.bed:md5,66cf1481b1e69fa4cf3b13f07efd8c40", + "sample4_2.chunk.1_local_density_error.txt:md5,2e2b91bbdd3225ebcd3402edf86a2cc6", + "sample4_2.chunk.1_polya.txt:md5,6fd5552e7b2152e3b46cdee04b140104", + "sample4_2.chunk.1_read.txt:md5,b0dc554a9b99c5f5b6fd3203f276c797", + "sample4_2.chunk.1_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_2.chunk.1_trans_read.bed:md5,347f03649d304377cb37dec40830d35c", + "sample4_2.chunk.1_trans_report.txt:md5,e2b7c12377d7a4424b253898f0f0bd7a", + "sample4_2.chunk.1_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_2.chunk.1_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample2.tsv:md5,5ee80b0a439ee6023faff9a0d555cfd8", + "sample3.tsv:md5,d40c004ff91279dd1227faf5a1706c0f", + "sample4.tsv:md5,3e3ef986b8eaaef1c062c5e3af27bcff", + "sample2.bed:md5,f587c4c86b185278b89f6495effde755", + "sample2_gene_report.txt:md5,17339982516a152b251fbe50d3bf9569", + "sample2_merge.txt:md5,82ed3779f378f72e292426fea41f7d65", + "sample2_trans_report.txt:md5,e8b352938adad13964a8dbbb4f0d0cea", + "sample3.bed:md5,33f6bd7b72aa2957bbf0ceffc9ff1b32", + "sample3_gene_report.txt:md5,275b49b66d41e337e420d73b40771851", + "sample3_merge.txt:md5,3988810f4afbeef5060e5f52555c8931", + "sample3_trans_report.txt:md5,d752c2a0cdcc8ca32ff5a54288bfc68c", + "sample4.bed:md5,66cf1481b1e69fa4cf3b13f07efd8c40", + "sample4_gene_report.txt:md5,88c1ef0edb49837b8c47806378a874a3", + "sample4_merge.txt:md5,48efa1d4c1bb408a8b26ba7c98cd2732", + "sample4_trans_report.txt:md5,02bc1176559b12d63fd186b3345e6007", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_lima_counts.txt:md5,d00757e4773f621db4f5459ca7a21088", + "multiqc_lima_summary.txt:md5,26fd02b7a09876ee334251e5afabc5b1" + ] + ], + "timestamp": "2026-08-14T15:11:45.900102927", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/inputs_map.nf.test b/tests/inputs_map.nf.test new file mode 100644 index 0000000..64eabf8 --- /dev/null +++ b/tests/inputs_map.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs map" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_map" + + test("-profile test_inputs_map") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_map.nf.test.snap b/tests/inputs_map.nf.test.snap new file mode 100644 index 0000000..f9a65c0 --- /dev/null +++ b/tests/inputs_map.nf.test.snap @@ -0,0 +1,153 @@ +{ + "-profile test_inputs_map": { + "content": [ + { + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + } + }, + [ + "06_MINIMAP2", + "06_MINIMAP2/sample4_0.chunk.1.bam", + "06_MINIMAP2/sample4_0.chunk.1.bam.bai", + "06_MINIMAP2/sample4_0.chunk.2.bam", + "06_MINIMAP2/sample4_0.chunk.2.bam.bai", + "06_MINIMAP2/sample4_0.chunk.3.bam", + "06_MINIMAP2/sample4_0.chunk.3.bam.bai", + "06_MINIMAP2/sample4_0.chunk.4.bam", + "06_MINIMAP2/sample4_0.chunk.4.bam.bai", + "06_MINIMAP2/sample4_0.chunk.5.bam", + "06_MINIMAP2/sample4_0.chunk.5.bam.bai", + "07_GSTAMA_COLLAPSE", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_read.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.1_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_read.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.2_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_read.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.3_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_read.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.4_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_read.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_0.chunk.5_variants.txt", + "08_GSTAMA_FILELIST", + "08_GSTAMA_FILELIST/sample4.tsv", + "09_GSTAMA_MERGE", + "09_GSTAMA_MERGE/sample4.bed", + "09_GSTAMA_MERGE/sample4_gene_report.txt", + "09_GSTAMA_MERGE/sample4_merge.txt", + "09_GSTAMA_MERGE/sample4_trans_report.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_isoseq_software_mqc_versions.yml" + ], + [ + "sample4_0.chunk.1_collapsed.bed:md5,33f6bd7b72aa2957bbf0ceffc9ff1b32", + "sample4_0.chunk.1_local_density_error.txt:md5,bde56c7c2c791918943ea8d6c8c2169a", + "sample4_0.chunk.1_polya.txt:md5,628ea62b918fc4f31e109f724d714a66", + "sample4_0.chunk.1_read.txt:md5,6ab436fef1e37907f89b19e07bfe3f1d", + "sample4_0.chunk.1_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_0.chunk.1_trans_read.bed:md5,19cdf0d7d935665da0f96b936c6affc6", + "sample4_0.chunk.1_trans_report.txt:md5,35610244e9d495e6f5dee1c6ae0580f8", + "sample4_0.chunk.1_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_0.chunk.1_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4_0.chunk.2_collapsed.bed:md5,05f7568e3d2f390e44f9f985b27247e2", + "sample4_0.chunk.2_local_density_error.txt:md5,7247a67bea9392c73ed5c4288bc66672", + "sample4_0.chunk.2_polya.txt:md5,434e6f3327bbeecd708dc6cc1edaa118", + "sample4_0.chunk.2_read.txt:md5,b643a3a994835b5c99e9bfe630aff856", + "sample4_0.chunk.2_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_0.chunk.2_trans_read.bed:md5,928ee441099b8c0d3c44054524603e94", + "sample4_0.chunk.2_trans_report.txt:md5,e0ae3f827531d7316f9397b4dbdb0667", + "sample4_0.chunk.2_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_0.chunk.2_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4_0.chunk.3_collapsed.bed:md5,844806f6d1979d68a3b9096267d7bf07", + "sample4_0.chunk.3_local_density_error.txt:md5,cda740cdf5b59aed316d23d97cccb9f4", + "sample4_0.chunk.3_polya.txt:md5,f5872c789c84037abd230f3e3053429e", + "sample4_0.chunk.3_read.txt:md5,d777caedc81cef340943c9e31cff3260", + "sample4_0.chunk.3_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_0.chunk.3_trans_read.bed:md5,c4e132389c86dc844e76f78c3724ed8d", + "sample4_0.chunk.3_trans_report.txt:md5,eb6a4b39128ce0c19a96b5df9bb00010", + "sample4_0.chunk.3_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_0.chunk.3_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4_0.chunk.4_collapsed.bed:md5,1abee63ee6b2ecd8a579fd293e9787bb", + "sample4_0.chunk.4_local_density_error.txt:md5,d35f24d3f83e2513bfd055cf3e438037", + "sample4_0.chunk.4_polya.txt:md5,9b1bb126d5f3ba8b1605fadec4f28d15", + "sample4_0.chunk.4_read.txt:md5,c827cfe75cf841613fe213d6d04a393f", + "sample4_0.chunk.4_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_0.chunk.4_trans_read.bed:md5,340aa905ab34937cf34d8434ad00ecc9", + "sample4_0.chunk.4_trans_report.txt:md5,0c43e570ac23818b1c183d48588deab1", + "sample4_0.chunk.4_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_0.chunk.4_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4_0.chunk.5_collapsed.bed:md5,1a8baa8613f6bdd0a0fa1ad7c38b7aaa", + "sample4_0.chunk.5_local_density_error.txt:md5,2a87123d2eb92f00ac730924b19dc2f8", + "sample4_0.chunk.5_polya.txt:md5,b5e129f170b71a74aae74120730ffdb1", + "sample4_0.chunk.5_read.txt:md5,ba943648c22434ac8ab663bb5ce2408e", + "sample4_0.chunk.5_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample4_0.chunk.5_trans_read.bed:md5,6f43624e2fad10e896ecd93011ae92ae", + "sample4_0.chunk.5_trans_report.txt:md5,5d6c4748d0b86d7b29cdf0d1f3e3cdf5", + "sample4_0.chunk.5_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample4_0.chunk.5_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample4.tsv:md5,38c9ea6c3c83932247b42fab1d07dbb3", + "sample4.bed:md5,4928c5cc59c23dd25486a22a9a5e9bed", + "sample4_gene_report.txt:md5,7e90720244d58d56e21c4c0285c576f3", + "sample4_merge.txt:md5,b91e9f22a1bd14324f3e378cdfb454c7", + "sample4_trans_report.txt:md5,27bc45fb5f585849fee71da6e951c99c", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" + ] + ], + "timestamp": "2026-08-14T15:12:33.973495948", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/inputs_multi_lib.nf.test b/tests/inputs_multi_lib.nf.test new file mode 100644 index 0000000..b30565e --- /dev/null +++ b/tests/inputs_multi_lib.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs multi_lib" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_multi_lib" + + test("-profile test_inputs_multi_lib") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_multi_lib.nf.test.snap b/tests/inputs_multi_lib.nf.test.snap new file mode 100644 index 0000000..0824702 --- /dev/null +++ b/tests/inputs_multi_lib.nf.test.snap @@ -0,0 +1,944 @@ +{ + "-profile test_inputs_multi_lib": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + }, + "PBCCS": { + "pbccs": "6.4.0" + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + "01_PBCCS/sample1_0.chunk1.metrics.json.gz", + "01_PBCCS/sample1_0.chunk1.report.json", + "01_PBCCS/sample1_0.chunk1.report.txt", + "01_PBCCS/sample1_0.chunk2.bam", + "01_PBCCS/sample1_0.chunk2.bam.pbi", + "01_PBCCS/sample1_0.chunk2.metrics.json.gz", + "01_PBCCS/sample1_0.chunk2.report.json", + "01_PBCCS/sample1_0.chunk2.report.txt", + "01_PBCCS/sample1_0.chunk3.bam", + "01_PBCCS/sample1_0.chunk3.bam.pbi", + "01_PBCCS/sample1_0.chunk3.metrics.json.gz", + "01_PBCCS/sample1_0.chunk3.report.json", + "01_PBCCS/sample1_0.chunk3.report.txt", + "01_PBCCS/sample1_0.chunk4.bam", + "01_PBCCS/sample1_0.chunk4.bam.pbi", + "01_PBCCS/sample1_0.chunk4.metrics.json.gz", + "01_PBCCS/sample1_0.chunk4.report.json", + "01_PBCCS/sample1_0.chunk4.report.txt", + "01_PBCCS/sample1_0.chunk5.bam", + "01_PBCCS/sample1_0.chunk5.bam.pbi", + "01_PBCCS/sample1_0.chunk5.metrics.json.gz", + "01_PBCCS/sample1_0.chunk5.report.json", + "01_PBCCS/sample1_0.chunk5.report.txt", + "01_PBCCS/sample1_1.chunk1.bam", + "01_PBCCS/sample1_1.chunk1.bam.pbi", + "01_PBCCS/sample1_1.chunk1.metrics.json.gz", + "01_PBCCS/sample1_1.chunk1.report.json", + "01_PBCCS/sample1_1.chunk1.report.txt", + "01_PBCCS/sample1_1.chunk2.bam", + "01_PBCCS/sample1_1.chunk2.bam.pbi", + "01_PBCCS/sample1_1.chunk2.metrics.json.gz", + "01_PBCCS/sample1_1.chunk2.report.json", + "01_PBCCS/sample1_1.chunk2.report.txt", + "01_PBCCS/sample1_1.chunk3.bam", + "01_PBCCS/sample1_1.chunk3.bam.pbi", + "01_PBCCS/sample1_1.chunk3.metrics.json.gz", + "01_PBCCS/sample1_1.chunk3.report.json", + "01_PBCCS/sample1_1.chunk3.report.txt", + "01_PBCCS/sample1_1.chunk4.bam", + "01_PBCCS/sample1_1.chunk4.bam.pbi", + "01_PBCCS/sample1_1.chunk4.metrics.json.gz", + 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"sample3_trans_report.txt:md5,6370921b9331122615415760360112fc", + "ccs-filter-graph.txt:md5,ba008b5846eef8b5fba1028bef4754d1", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_general_stats.txt:md5,2fa069b074cad309312a2cc03006d98d", + "multiqc_lima_counts.txt:md5,d00757e4773f621db4f5459ca7a21088", + "multiqc_lima_summary.txt:md5,4aa9cb449edee79805d6caaf23fe5fd2" + ] + ], + "timestamp": "2026-08-14T15:17:15.255981647", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/inputs_refine.nf.test b/tests/inputs_refine.nf.test new file mode 100644 index 0000000..41fc011 --- /dev/null +++ b/tests/inputs_refine.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs refine" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_refine" + + test("-profile test_inputs_refine") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_refine.nf.test.snap b/tests/inputs_refine.nf.test.snap new file mode 100644 index 0000000..5f82c7b --- /dev/null +++ b/tests/inputs_refine.nf.test.snap @@ -0,0 +1,126 @@ +{ + "-profile test_inputs_refine": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + } + }, + [ + "03_ISOSEQ_REFINE", + "03_ISOSEQ_REFINE/sample3_0.bam", + "03_ISOSEQ_REFINE/sample3_0.bam.pbi", + "03_ISOSEQ_REFINE/sample3_0.consensusreadset.xml", + "03_ISOSEQ_REFINE/sample3_0.filter_summary.report.json", + "03_ISOSEQ_REFINE/sample3_0.report.csv", + "04_BAMTOOLS_CONVERT", + "04_BAMTOOLS_CONVERT/sample3_0.fasta", + "05_GSTAMA_POLYACLEANUP", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama_tails.fa.gz", + "06_MINIMAP2", + "06_MINIMAP2/sample3_0.chunk.1.bam", + "06_MINIMAP2/sample3_0.chunk.1.bam.bai", + "06_MINIMAP2/sample3_0.chunk.2.bam", + "06_MINIMAP2/sample3_0.chunk.2.bam.bai", + "07_GSTAMA_COLLAPSE", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_polya.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_read.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_varcov.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_variants.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_polya.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_read.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_varcov.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_variants.txt", + "08_GSTAMA_FILELIST", + "08_GSTAMA_FILELIST/sample3.tsv", + "09_GSTAMA_MERGE", + "09_GSTAMA_MERGE/sample3.bed", + "09_GSTAMA_MERGE/sample3_gene_report.txt", + "09_GSTAMA_MERGE/sample3_merge.txt", + "09_GSTAMA_MERGE/sample3_trans_report.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_isoseq_software_mqc_versions.yml" + ], + [ + "sample3_0.bam.pbi:md5,afb9a61ed9f3aa3f589af5c48a2f9f45", + "sample3_0.report.csv:md5,8d350f8dba8c928ec8b693f47dc1c096", + "sample3_0.fasta:md5,81b607067bac48a5b53281e982acd623", + "sample3_0.chunk.1_tama.fa.gz:md5,547bcdc2de2cffc24b5fcc1b5a13bb2f", + "sample3_0.chunk.1_tama_polya_flnc_report.txt.gz:md5,d5181d0e3cd99b207032729e345bec15", + "sample3_0.chunk.1_tama_tails.fa.gz:md5,db16b89e4737e9a27ca5d8ac7816abba", + "sample3_0.chunk.2_tama.fa.gz:md5,eeabbdacda87cf5bfa23b530d4e1a838", + "sample3_0.chunk.2_tama_polya_flnc_report.txt.gz:md5,8e2996f18473044831036113c804b1c3", + "sample3_0.chunk.2_tama_tails.fa.gz:md5,397d55c45160ffe3a2596a77ec3104f4", + "sample3_0.chunk.1_collapsed.bed:md5,33f6bd7b72aa2957bbf0ceffc9ff1b32", + "sample3_0.chunk.1_local_density_error.txt:md5,bde56c7c2c791918943ea8d6c8c2169a", + "sample3_0.chunk.1_polya.txt:md5,628ea62b918fc4f31e109f724d714a66", + "sample3_0.chunk.1_read.txt:md5,f3fd6b182d7255f35339a0507cd55564", + "sample3_0.chunk.1_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample3_0.chunk.1_trans_read.bed:md5,19cdf0d7d935665da0f96b936c6affc6", + "sample3_0.chunk.1_trans_report.txt:md5,35610244e9d495e6f5dee1c6ae0580f8", + "sample3_0.chunk.1_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample3_0.chunk.1_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample3_0.chunk.2_collapsed.bed:md5,33f6bd7b72aa2957bbf0ceffc9ff1b32", + "sample3_0.chunk.2_local_density_error.txt:md5,50da2e01c5aeb64595e8aba8957a74d7", + "sample3_0.chunk.2_polya.txt:md5,628ea62b918fc4f31e109f724d714a66", + "sample3_0.chunk.2_read.txt:md5,e8b06298d18b442a1b5b2fe1d2fb94e0", + "sample3_0.chunk.2_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample3_0.chunk.2_trans_read.bed:md5,244ba6d15cbf8bd84d6e3b5d005017dd", + "sample3_0.chunk.2_trans_report.txt:md5,35610244e9d495e6f5dee1c6ae0580f8", + "sample3_0.chunk.2_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample3_0.chunk.2_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample3.tsv:md5,13594e213bd42a105685200e9d4afbfa", + "sample3.bed:md5,2376959ce39530c95f0782741d058662", + "sample3_gene_report.txt:md5,9fc021aed668882970918e34c80f33a5", + "sample3_merge.txt:md5,4d9f5af63bf3cbeec576b19fdaddfa56", + "sample3_trans_report.txt:md5,166e969a66faeb156a59250cc2c1d228", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" + ] + ], + "timestamp": "2026-08-14T15:18:11.073851011", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/inputs_refine_map.nf.test b/tests/inputs_refine_map.nf.test new file mode 100644 index 0000000..80e47a1 --- /dev/null +++ b/tests/inputs_refine_map.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline inputs refine map" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_inputs_refine_map" + + test("-profile test_inputs_refine_map") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/inputs_refine_map.nf.test.snap b/tests/inputs_refine_map.nf.test.snap new file mode 100644 index 0000000..43c4da4 --- /dev/null +++ b/tests/inputs_refine_map.nf.test.snap @@ -0,0 +1,236 @@ +{ + "-profile test_inputs_refine_map": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + } + }, + [ + "03_ISOSEQ_REFINE", + "03_ISOSEQ_REFINE/sample3_0.bam", + "03_ISOSEQ_REFINE/sample3_0.bam.pbi", + "03_ISOSEQ_REFINE/sample3_0.consensusreadset.xml", + "03_ISOSEQ_REFINE/sample3_0.filter_summary.report.json", + "03_ISOSEQ_REFINE/sample3_0.report.csv", + "04_BAMTOOLS_CONVERT", + "04_BAMTOOLS_CONVERT/sample3_0.fasta", + "05_GSTAMA_POLYACLEANUP", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.1_tama_tails.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama.fa.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama_polya_flnc_report.txt.gz", + "05_GSTAMA_POLYACLEANUP/sample3_0.chunk.2_tama_tails.fa.gz", + "06_MINIMAP2", + "06_MINIMAP2/sample3_0.chunk.1.bam", + "06_MINIMAP2/sample3_0.chunk.1.bam.bai", + "06_MINIMAP2/sample3_0.chunk.2.bam", + "06_MINIMAP2/sample3_0.chunk.2.bam.bai", + "06_MINIMAP2/sample4_1.chunk.1.bam", + "06_MINIMAP2/sample4_1.chunk.1.bam.bai", + "06_MINIMAP2/sample4_1.chunk.2.bam", + "06_MINIMAP2/sample4_1.chunk.2.bam.bai", + "06_MINIMAP2/sample4_1.chunk.3.bam", + "06_MINIMAP2/sample4_1.chunk.3.bam.bai", + "06_MINIMAP2/sample4_1.chunk.4.bam", + "06_MINIMAP2/sample4_1.chunk.4.bam.bai", + "06_MINIMAP2/sample4_1.chunk.5.bam", + "06_MINIMAP2/sample4_1.chunk.5.bam.bai", + "07_GSTAMA_COLLAPSE", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_polya.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_read.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_varcov.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.1_variants.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_polya.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_read.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_varcov.txt", + "07_GSTAMA_COLLAPSE/sample3_0.chunk.2_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_read.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.1_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_read.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.2_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_read.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.3_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_read.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.4_variants.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_collapsed.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_local_density_error.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_polya.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_read.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_strand_check.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_trans_read.bed", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_trans_report.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_varcov.txt", + "07_GSTAMA_COLLAPSE/sample4_1.chunk.5_variants.txt", + "08_GSTAMA_FILELIST", + "08_GSTAMA_FILELIST/sample3.tsv", + "08_GSTAMA_FILELIST/sample4.tsv", + "09_GSTAMA_MERGE", + "09_GSTAMA_MERGE/sample3.bed", + "09_GSTAMA_MERGE/sample3_gene_report.txt", + "09_GSTAMA_MERGE/sample3_merge.txt", + "09_GSTAMA_MERGE/sample3_trans_report.txt", + "09_GSTAMA_MERGE/sample4.bed", + 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b/tests/minimap2.nf.test new file mode 100644 index 0000000..c60b4cf --- /dev/null +++ b/tests/minimap2.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline - Minimap2 path" + script "../main.nf" + tag "pipeline" + tag "pipeline_isoseq" + profile "test_minimap2" + + test("-profile test_minimap2") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeFromYamlMap("${outputDir}/pipeline_info/nf_core_isoseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/minimap2.nf.test.snap b/tests/minimap2.nf.test.snap new file mode 100644 index 0000000..c5c0e3b --- /dev/null +++ b/tests/minimap2.nf.test.snap @@ -0,0 +1,398 @@ +{ + "-profile test_minimap2": { + "content": [ + { + "BAMTOOLS_CONVERT": { + "bamtools": "2.5.2" + }, + "GSTAMA_COLLAPSE": { + "gstama": 20211103 + }, + "GSTAMA_MERGE": { + "gstama": "0.0.1" + }, + "GSTAMA_POLYACLEANUP": { + "gstama": 20211103 + }, + "ISOSEQ_REFINE": { + "isoseq": "4.0.0" + }, + "LIMA": { + "lima": "2.12.0" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.30-r1287" + }, + "PBCCS": { + "pbccs": "6.4.0" + } + }, + [ + "01_PBCCS", + "01_PBCCS/sample1_0.chunk1.bam", + "01_PBCCS/sample1_0.chunk1.bam.pbi", + "01_PBCCS/sample1_0.chunk1.metrics.json.gz", + 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"sample1_0.chunk5_local_density_error.txt:md5,2a87123d2eb92f00ac730924b19dc2f8", + "sample1_0.chunk5_polya.txt:md5,b5e129f170b71a74aae74120730ffdb1", + "sample1_0.chunk5_read.txt:md5,6fc5c8520a8bb47cc549376f5e32ce3b", + "sample1_0.chunk5_strand_check.txt:md5,42cc52b2660b1e0b84e1c9ab37a965ec", + "sample1_0.chunk5_trans_read.bed:md5,6f43624e2fad10e896ecd93011ae92ae", + "sample1_0.chunk5_trans_report.txt:md5,5d6c4748d0b86d7b29cdf0d1f3e3cdf5", + "sample1_0.chunk5_varcov.txt:md5,7b77861fe5e8e953d6d193ace2467e12", + "sample1_0.chunk5_variants.txt:md5,a4c518e1dfb7ff762bd7e5c3d7370986", + "sample1.tsv:md5,54b9ee29a34d402185285211b673b9c4", + "sample1.bed:md5,4928c5cc59c23dd25486a22a9a5e9bed", + "sample1_gene_report.txt:md5,c698958ea806a156847961b0c719a66c", + "sample1_merge.txt:md5,07cdfbf4070903d66ffe459f9ce94715", + "sample1_trans_report.txt:md5,e40712d885417415a654adaed0c34c08", + "ccs-filter-graph.txt:md5,9f35c8022cdae8ef48f9047e67111bd1", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_general_stats.txt:md5,f60e94deef7b1d8f6f4c5e67b325e6ba", + "multiqc_lima_counts.txt:md5,a2e8e8ca0c68cb43d2887b196d251ca4", + "multiqc_lima_summary.txt:md5,11e5253acb7b8d344a4747f5796cf995" + ] + ], + "timestamp": "2026-08-14T15:21:28.964625469", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + } +} \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 0000000..3af4a96 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,15 @@ +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// TODO nf-core: Specify any additional parameters here +// Or any resources requirements +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/' +} + +// Fixes S3 access issues on self-hosted runners +aws.client.anonymous = true diff --git a/workflows/isoseq.nf b/workflows/isoseq.nf index 22b5b17..f7270df 100644 --- a/workflows/isoseq.nf +++ b/workflows/isoseq.nf @@ -3,29 +3,12 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_isoseq_pipeline' -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) -//ch_multiqc_config = [ -// file("$projectDir/assets/multiqc_config.yml" , checkIfExists: true), -// file("$projectDir/assets/nf-core-isoseq_logo_light.png", checkIfExists: true) -// ] -//ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT LOCAL MODULES/SUBWORKFLOWS @@ -35,15 +18,18 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { SET_CHUNK_NUM_CHANNEL } from '../subworkflows/local/set_chunk_num_channel' -include { SET_VALUE_CHANNEL as SET_FASTA_CHANNEL } from '../subworkflows/local/set_value_channel' -include { SET_VALUE_CHANNEL as SET_GTF_CHANNEL } from '../subworkflows/local/set_value_channel' -include { SET_VALUE_CHANNEL as SET_PRIMERS_CHANNEL } from '../subworkflows/local/set_value_channel' +include { SET_CHUNK_NUM_CHANNEL } from '../subworkflows/local/set_chunk_num_channel/main' +include { SET_VALUE_CHANNEL as SET_FASTA_CHANNEL } from '../subworkflows/local/set_value_channel/main' +include { SET_VALUE_CHANNEL as SET_GTF_CHANNEL } from '../subworkflows/local/set_value_channel/main' +include { SET_VALUE_CHANNEL as SET_PRIMERS_CHANNEL } from '../subworkflows/local/set_value_channel/main' +include { CHUNKER as CHUNKER_BAMTOOLS_OUT } from '../subworkflows/local/chunker/main' +include { CHUNKER as CHUNKER_INPUT_FASTAS } from '../subworkflows/local/chunker/main' // // MODULE: Local to the pipeline // -include { GSTAMA_FILELIST } from '../modules/local/gstama/filelist/main' +include { GSTAMA_FILELIST } from '../modules/local/gstama/filelist/main' +include { GSTAMA_FILELIST as GSTAMA_FILELIST_ALL } from '../modules/local/gstama/filelist/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -54,19 +40,19 @@ include { GSTAMA_FILELIST } from '../modules/local/gstama/filelist/main' // // MODULE: Installed directly from nf-core/modules // -include { PBCCS } from '../modules/nf-core/pbccs/main' -include { LIMA } from '../modules/nf-core/lima/main' -include { ISOSEQ_REFINE } from '../modules/nf-core/isoseq/refine/main' -include { BAMTOOLS_CONVERT } from '../modules/nf-core/bamtools/convert/main' -include { GSTAMA_POLYACLEANUP } from '../modules/nf-core/gstama/polyacleanup/main' -include { GUNZIP } from '../modules/nf-core/gunzip/main' -include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' -include { GNU_SORT } from '../modules/nf-core/gnu/sort/main' -include { ULTRA_INDEX } from '../modules/nf-core/ultra/index/main' -include { ULTRA_ALIGN } from '../modules/nf-core/ultra/align/main' -include { GSTAMA_COLLAPSE } from '../modules/nf-core/gstama/collapse/main' -include { GSTAMA_MERGE } from '../modules/nf-core/gstama/merge/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] ) +include { PBCCS } from '../modules/nf-core/pbccs/main' +include { LIMA } from '../modules/nf-core/lima/main' +include { ISOSEQ_REFINE } from '../modules/nf-core/isoseq/refine/main' +include { BAMTOOLS_CONVERT } from '../modules/nf-core/bamtools/convert/main' +include { GSTAMA_POLYACLEANUP } from '../modules/nf-core/gstama/polyacleanup/main' +include { GUNZIP } from '../modules/nf-core/gunzip/main' +include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' +include { GNU_SORT } from '../modules/nf-core/gnu/sort/main' +include { ULTRA_INDEX } from '../modules/nf-core/ultra/index/main' +include { ULTRA_ALIGN } from '../modules/nf-core/ultra/align/main' +include { GSTAMA_COLLAPSE } from '../modules/nf-core/gstama/collapse/main' +include { GSTAMA_MERGE } from '../modules/nf-core/gstama/merge/main' +include { GSTAMA_MERGE as GSTAMA_MERGE_ALL } from '../modules/nf-core/gstama/merge/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -77,89 +63,150 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft workflow ISOSEQ { take: - ch_samplesheet - + ch_samplesheet // channel: samplesheet read in from --input + multiqc_config + multiqc_logo + multiqc_methods_description + outdir main: - // - // SET UP VERSIONS CHANNELS - // - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + // Set version and multiqc channels + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() - // - // START PIPELINE - // - // Prepare channels for: - SET_FASTA_CHANNEL(params.fasta) // - genome fasta - SET_PRIMERS_CHANNEL(params.primers) // - primers fasta + // Value channels initialization + SET_FASTA_CHANNEL(params.fasta) // genome fasta + ch_primers = channel.empty() // primers fasta + if (params.primers) { + SET_PRIMERS_CHANNEL(params.primers) // primers fasta + ch_primers = SET_PRIMERS_CHANNEL.out.data + } if (params.aligner == "ultra") { - SET_GTF_CHANNEL(params.gtf) // - genome gtf + SET_GTF_CHANNEL(params.gtf) // genome gtf } - -// ISOSEQ pipeline entrypoint ################################################################## - if (params.entrypoint == "isoseq") { - - SET_CHUNK_NUM_CHANNEL(params.input, params.chunk) // - PBCCS parallelization - - PBCCS(ch_samplesheet, SET_CHUNK_NUM_CHANNEL.out.chunk_num, params.chunk) // Generate CCS from raw reads - PBCCS.out.bam // Update meta: update id (+chunkX) and store former id - .map { - def chk = (it[1] =~ /.*\.(chunk\d+)\.bam/)[ 0 ][ 1 ] - def id_former = it[0].id - def id_new = it[0].id + "." + chk - return [ [id:id_new, id_former:id_former, single_end:true], it[1] ] + // Dispatch inputs to redistribute them to their ad hoc starting point + ch_samplesheet + .branch { meta, _seq_data, _pbi -> + ccs : meta.start_from == "ccs" + lima : meta.start_from == "lima" + refine : meta.start_from == "refine" + mapping: meta.start_from == "mapping" } - .set { ch_pbccs_bam_updated } - - LIMA(ch_pbccs_bam_updated, SET_PRIMERS_CHANNEL.out.data) // Remove primers from CCS - ISOSEQ_REFINE(LIMA.out.bam, SET_PRIMERS_CHANNEL.out.data) // Discard CCS without polyA tails, remove it from the other - BAMTOOLS_CONVERT(ISOSEQ_REFINE.out.bam) // Convert bam to fasta - GSTAMA_POLYACLEANUP(BAMTOOLS_CONVERT.out.data) // Clean polyA tails from reads - } - - -// MAP pipeline entrypoint ################################################################## - if (params.entrypoint == "isoseq") { - ch_reads_to_map = GSTAMA_POLYACLEANUP.out.fasta - } - else if (params.entrypoint == "map") { - ch_reads_to_map = ch_samplesheet - } - + .set { ch_seq_data } + // ch_seq_data.ccs.view { it -> "BRANCH: ccs : $it" } + // ch_seq_data.lima.view { it -> "BRANCH: lima : $it" } + // ch_seq_data.refine.view { it -> "BRANCH: refine : $it" } + // ch_seq_data.mapping.view{ it -> "BRANCH: mapping: $it" } + + // PBCCS: prepare and run ccs + SET_CHUNK_NUM_CHANNEL(params.input, params.chunk_ccs) // - PBCCS parallelization + + PBCCS( + ch_seq_data.ccs, + SET_CHUNK_NUM_CHANNEL.out.chunk_num, + params.chunk_ccs) // Generate CCS from raw reads + + PBCCS.out.bam // Update meta: update id (+chunkX) and store former id + .map { meta, file -> + def chk = (file =~ /.*\.(chunk\d+)\.bam/)[0][1] + def id_former = meta.id + def id_new = meta.id + "." + chk + return [ [id:id_new, id_former:id_former, single_end:true], file ] + } + .set { ch_pbccs_out_bam_updated } + + // LIMA: Add the samplesheet's LIMA inputs to the queue and run lima + ch_pbccs_out_bam_updated + .concat(ch_seq_data.lima.map { meta, bam, _pbi -> [ meta, bam ] }) + .set { ch_lima_input } + // ch_lima_input.view { meta, bam -> println("ch_lima_input: $meta | $bam") } + LIMA(ch_lima_input, ch_primers) // Remove primers from CCS + + // LIMA: Add the samplesheet's refine inputs to the queue and run isoseq refine + LIMA.out.bam + .concat(ch_seq_data.refine.map { meta, bam, _pbi -> [ meta, bam ] }) + .set { ch_isoseq_refine_input } + // ch_isoseq_refine_input.view { meta, bam -> println("ch_isoseq_refine_input: $meta | $bam") } + ISOSEQ_REFINE(ch_isoseq_refine_input, ch_primers) // Discard CCS without polyA tails, remove it from the other + + // Convert bam files to fasta + BAMTOOLS_CONVERT(ISOSEQ_REFINE.out.bam) // Convert bam to fasta + // BAMTOOLS_CONVERT.out.data.view { meta, fa -> println("BAMTOOLS_CONVERT.out.data: $meta | $fa") } + + // Split fastas into chunks + CHUNKER_BAMTOOLS_OUT(BAMTOOLS_CONVERT.out.data, params.chunk_mapping, false, false) // false, false == no need to decompress input, don't compress output + // CHUNKER_BAMTOOLS_OUT.out.fastas.view { meta, fa -> println("CHUNKER_BAMTOOLS_OUT.out.fasta: $meta | $fa") } + + // GSTAMA_POLYACLEANUP: Convert to fasta and run polyAcleanup + GSTAMA_POLYACLEANUP(CHUNKER_BAMTOOLS_OUT.out.fastas) // Clean polyA tails from reads + // GSTAMA_POLYACLEANUP.out.fasta.view { meta, fa -> println("GSTAMA_POLYACLEANUP.out.fasta: $meta | $fa") } + + // Split user fasta and add them the main channel + CHUNKER_INPUT_FASTAS(ch_seq_data.mapping.map { meta, fasta, _pbi -> [ meta, fasta ] }, params.chunk_mapping, true, false) + // CHUNKER_INPUT_FASTAS.out.fastas.view { meta, fa -> println("CHUNKER_INPUT_FASTAS.out.fasta: $meta | $fa") } + + // MAPPING: Split samplesheet's fasta files, add them to the queue and run mapping + GSTAMA_POLYACLEANUP.out.fasta + .concat(CHUNKER_INPUT_FASTAS.out.fastas) + .set { ch_input_fastas } + // ch_input_fastas.view { meta, fa -> println("ch_input_fastas.out.fasta: $meta | $fa") } // Align FLNCs: User can choose between minimap2 and uLTRA aligners if (params.aligner == "ultra") { - GNU_SORT(SET_GTF_CHANNEL.out.data.map { it -> [ [id:'genome'], it ] } ) // Sort GTF on sequence and start, uLTRA index fails with topological sort - ULTRA_INDEX(SET_FASTA_CHANNEL.out.data, GNU_SORT.out.sorted.map { it[1] }) // Index GTF file before alignment - GUNZIP(ch_reads_to_map) // uncompress fastas (gz not supported by uLTRA) - ULTRA_ALIGN(GUNZIP.out.gunzip, SET_FASTA_CHANNEL.out.data, ULTRA_INDEX.out.index) // Align read against genome - GSTAMA_COLLAPSE(ULTRA_ALIGN.out.bam, SET_FASTA_CHANNEL.out.data) // Clean gene models + GNU_SORT(SET_GTF_CHANNEL.out.data.map { it -> [ [id:'genome'], it, 'gtf' ] } ) // Sort GTF on sequence and start, uLTRA index fails with topological sort + ULTRA_INDEX( // Index GTF file before alignment + SET_FASTA_CHANNEL.out.data.map { it -> [ [id:'genome'], it ] }, + GNU_SORT.out.sorted) + GUNZIP(ch_input_fastas) // uncompress fastas (gz not supported by uLTRA) + + // The ultra index channel must be the same size as the reads/GUNZIP channel. + // join: gather all index files into one channel + // combine: duplicates index tuples to match number of reads + // map: remove read and its meta as we don't need them + ch_ultra_index = + ULTRA_INDEX.out.pickle + .join(ULTRA_INDEX.out.database) + .combine(GUNZIP.out.gunzip) + .map { meta1, pickle, db, _meta2, _reads -> [ meta1, pickle, db ] } + + ULTRA_ALIGN( + GUNZIP.out.gunzip, + SET_FASTA_CHANNEL.out.data.map { it -> [ [id:'genome'], it ] }, + ch_ultra_index) // Align read against genome + GSTAMA_COLLAPSE(ULTRA_ALIGN.out.bam, SET_FASTA_CHANNEL.out.data) // Clean gene models } else if (params.aligner == "minimap2") { MINIMAP2_ALIGN( // Align read against genome - ch_reads_to_map, - [ [id:"Dummy"], file(params.fasta) ], - Channel.value(true), - Channel.value("bai"), - Channel.value(false), - Channel.value(false)) + ch_input_fastas, + [ [id:'genome'], file(params.fasta) ], + channel.value(true), + channel.value("bai"), + channel.value(false), + channel.value(false)) GSTAMA_COLLAPSE(MINIMAP2_ALIGN.out.bam, SET_FASTA_CHANNEL.out.data) // Clean gene models } GSTAMA_COLLAPSE.out.bed // replace id with the former sample id and group files by sample - .map { [ [id:it[0].id_former], it[1] ] } + .map { meta, file -> + def sample = meta.id_former.replaceAll(/_\d+/, '') + [ + [ id:sample ], + file + ] + } .groupTuple() .set { ch_tcollapse } - cap_value = params.capped == true ? Channel.value("capped") : Channel.value("no_cap") + // ch_tcollapse.view { meta, fa -> println("ch_tcollapse: $meta | $fa") } + + cap_value = params.capped == true ? channel.value("capped") : channel.value("no_cap") GSTAMA_FILELIST( // Generate the filelist file needed by TAMA merge ch_tcollapse, cap_value, - Channel.value("1,1,1")) + channel.value("1,1,1")) ch_tcollapse // Synchronized bed files produced by TAMA collapse with file list file generated by GSTAMA_FILELIST .join( GSTAMA_FILELIST.out.tsv ) @@ -167,86 +214,95 @@ workflow ISOSEQ { GSTAMA_MERGE(ch_tmerge_in.map { [ it[0], it[1] ] }, ch_tmerge_in.map { it[2] }) // Merge all bed files from one sample into a uniq bed file + // Merge all bed files from all samples into a uniq bed file + ( params.tama_merge_all ? GSTAMA_MERGE.out.bed : channel.empty() ) + .map { _meta, bed -> [ [ id: "all_samples" ], bed ] } + .groupTuple() + .filter { _meta, beds -> beds.size() > 1 } // Only merge if there are more than one bed file + .set { ch_merge_all_filelist_input } - // - // MODULE: Pipeline reporting - // - if (params.entrypoint == "isoseq") { - ch_versions = ch_versions.mix(PBCCS.out.versions) - ch_versions = ch_versions.mix(LIMA.out.versions) - ch_versions = ch_versions.mix(ISOSEQ_REFINE.out.versions) - ch_versions = ch_versions.mix(BAMTOOLS_CONVERT.out.versions) - ch_versions = ch_versions.mix(GSTAMA_POLYACLEANUP.out.versions) - } + GSTAMA_FILELIST_ALL( + ch_merge_all_filelist_input, + cap_value, + channel.value("1,1,1") + ) - if (params.aligner == "ultra") { - ch_versions = ch_versions.mix(GNU_SORT.out.versions) - ch_versions = ch_versions.mix(ULTRA_INDEX.out.versions) - ch_versions = ch_versions.mix(ULTRA_ALIGN.out.versions) - } - else if (params.aligner == "minimap2") { - ch_versions = ch_versions.mix(MINIMAP2_ALIGN.out.versions) - } + ch_merge_all_filelist_input + .join( GSTAMA_FILELIST_ALL.out.tsv ) + .set { ch_tmerge_all_in } - ch_versions = ch_versions.mix(GSTAMA_COLLAPSE.out.versions) - ch_versions = ch_versions.mix(GSTAMA_MERGE.out.versions) + GSTAMA_MERGE_ALL( + ch_tmerge_all_in.map { meta, beds, _list -> [ meta, beds ] }, + ch_tmerge_all_in.map { _meta, _beds, list -> list } + ) // - // MODULE: CUSTOM_DUMPSOFTWAREVERSIONS + // Collate and save software versions // - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + def topic_versions = channel.topic("versions") + .distinct() + .branch { entry -> + versions_file: entry instanceof Path + versions_tuple: true + } + + def topic_versions_string = topic_versions.versions_tuple + .map { process, tool, version -> + [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] + } + .groupTuple(by:0) + .map { process, tool_versions -> + tool_versions.unique().sort() + "${process}:\n${tool_versions.join('\n')}" + } + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + .mix(topic_versions_string) + .collectFile( + storeDir: "${outdir}/pipeline_info", + name: 'nf_core_' + 'isoseq_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ) // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - if (params.entrypoint == "isoseq") { - ch_multiqc_files = ch_multiqc_files.mix(PBCCS.out.report_json.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.summary.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.counts.collect{it[1]}.ifEmpty([])) - } - - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - + ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - // ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - // ch_multiqc_files = ch_multiqc_files.mix( - // ch_methods_description.collectFile( - // name: 'methods_description_mqc.yaml', - // sort: true - // ) - // ) + ch_multiqc_custom_methods_description = multiqc_methods_description ? + file(multiqc_methods_description, checkIfExists: true) : + file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = channel.value( + methodsDescriptionText(ch_multiqc_custom_methods_description)) + + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) + + ch_multiqc_files = ch_multiqc_files.mix(PBCCS.out.report_json.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.summary.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.counts.collect{it[1]}.ifEmpty([])) MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - channel.empty(), - channel.empty() + ch_multiqc_files.flatten().collect().map { files -> + [ + [ id: 'isoseq' ], + files, + multiqc_config + ? file(multiqc_config, checkIfExists: true) + : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), + multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [], + [], + [], + ] + } ) emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] }
    Process Name \\", - " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls