snakemake / 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.

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'