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'