Conversation
Important! Template update for nf-core/tools v3.1.1
Added an optional field `bam_type` to allow simultaneous input of both Subreads and CCS sequences
Added parameter `skip_lima`
Added parameter `tama_merge_all`
added 10 commits
August 7, 2026 16:14
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
|
❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
added 17 commits
August 11, 2026 15:44
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
PacBio technology has evolved, and the pipeline must follow.
I have been lucky to be involved in an Iso-Seq project which allowed me to work on the
pipeline again.
Sequencing providers used to deliver raw subreads. Nowadays the sequencing machines compute
the consensus themselves and deliver primer-free Circular Consensus Sequences directly to
the client. This major release adapts to that: an analysis can now start from the CCS, LIMA,
isoseq refineor mapping step.The new samplesheet format introduced in version 3 lets you choose the starting step for
each listed library. Alongside it, data chunking is now controlled by two options:
chunk_ccs— controls chunking of the CCS stepchunk_mapping— splits provided FASTA files for mapping and annotation onlyWarning
This is a major release with breaking changes. Samplesheets and command lines written
for v2.0.0 will not work unmodified.
sample,seq_data,pbi,start_from, replacingsample,bam,pbi,reads--entrypointremoved — the entry point is declared per row viastart_from--chunksplit into--chunk_ccsand--chunk_mapping--max_cpus,--max_memory,--max_timeremoved (useresourceLimitsin a config)Migration instructions in usage.md
--primersis also no longer unconditionally required — it is needed only when at least onerow starts from
ccs,limaorrefine.Version 2.1.0 was drafted but never released; its changes are included here, which is why
the version goes from 2.0.0 straight to 3.0.0.
Closes #57
Closes #50
Refs #48
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).