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git-pull-request

GitHub Action

snakemake

v1.25.1 Latest version

snakemake

git-pull-request

snakemake

Run Snakemake on the repository

Installation

Copy and paste the following snippet into your .yml file.

 
              
- name: snakemake

              
  uses: snakemake/snakemake-github-action@v1.25.1
Learn more about this action in snakemake/snakemake-github-action

Choose a version

Snakemake github action

This action runs Snakemake on the repository.

Inputs

directory

Required The working directory to use. Default .test.

snakefile

The Snakefile containing the workflow description. Default Snakefile.

args

Additional arguments to pass to Snakemake.

stagein

Preliminary commands to run before the workflow execution.

task

Whether to run Snakemake or to generate a container image specification (in the form of a Dockerfile) that contains all required environments. Can be either run or containerize. Default run.

show-disk-usage-on-error

Whether used disk space shall be printed if Snakemake fails. Can be either true or false (default: false).

Example usage

- name: Linting
  uses: snakemake/snakemake-github-action@v1
  with:
    directory: '.test'
    snakefile: 'workflow/Snakefile'
    args: '--lint'

- name: Testing
  uses: snakemake/snakemake-github-action@v1
  with:
    directory: '.test'
    snakefile: 'workflow/Snakefile'
    args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
    stagein: '' # additional preliminary commands to run (can be multiline)
    show-disk-usage-on-error: true


- name: Create container file
  uses: snakemake/snakemake-github-action@v1
  with:
    snakefile: 'workflow/Snakefile'
    task: 'containerize'