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Snakemake example

This repository contains example workflows for Snakemake.

Usage on NeSI

Log in Mahuika, then load the Snakemake environment module:

module purge && module load snakemake/7.6.2-gimkl-2020a-Python-3.9.9

Then clone this repository:

git clone https://github.com/jennan/snakemake_example.git

Switch to the directory of the workflow of interest, for example input_function:

cd snakemake_example/input_function

Run the workflow with desired number of cores:

snakemake -c 1

Example Workflows

The following examples are available:

  • input_function showcases a workflow using an input function.
  • checkpoint illustrates a workflow using checkpoints for data-dependent workflows.
  • docker shows how to use Docker containers, directly fetching them from a registry.
  • slurm provides the core elements to run a workflow using Slurm on NeSI and using a Docker container.
  • slurm_immediate showcases an alternative way to run a workflow using Slurm, submitting all jobs at once.
  • slurm_sync presents another alternative to run a workflow using Slurm, using srun directly.
  • restart presents a workflow with a failing rule that can be restarted.
  • conda provides a workflow using a Conda environment.
  • unzip presents a workflow unzipping an archive, using the content and discarding intermediate files.