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git-pull-request

GitHub Action

snakemake

v1.6.1

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/[email protected]
Learn more about this action in snakemake/snakemake-github-action

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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.

Example usage

- name: Linting
  uses: snakemake/[email protected]
  with:
    directory: '.test'
    snakefile: 'workflow/Snakefile'
    args: '--lint'
- name: Testing
  uses: snakemake/[email protected]
  with:
    directory: '.test'
    snakefile: 'workflow/Snakefile'
    args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
    stagein: '' # additional preliminary commands to run (can be multiline)