colinbrislawn / snakemake-github-action

A Github action for running a Snakemake workflow

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

uses: snakemake/snakemake-github-action@v1.4.0
with:
  directory: '.test'
  snakefile: 'workflow/Snakefile'
  args: '--use-conda'
  stagein: '' # additional preliminary commands to run (can be multiline)