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).

snakemake-version

Snakemake version to install from conda. Default * (latest available version from the configured channels).

snakemake-branch

Optional Snakemake git branch to install from https://github.com/snakemake/snakemake. If set, this takes precedence over snakemake-version and Snakemake is installed from source via pip.

Example usage

- name: Linting
  uses: snakemake/snakemake-github-action@v2
  with:
    directory: ".test"
    snakefile: "workflow/Snakefile"
    args: "--lint"

- name: Testing
  uses: snakemake/snakemake-github-action@v2
  with:
    directory: ".test"
    snakefile: "workflow/Snakefile"
    args: "--cores 1 --sdm conda --conda-cleanup-pkgs cache"
    stagein: "" # additional preliminary commands to run (can be multiline)
    show-disk-usage-on-error: true

- name: Testing with custom Snakemake branch
  uses: snakemake/snakemake-github-action@v2
  with:
    directory: ".test"
    snakefile: "workflow/Snakefile"
    args: "--cores 1 --sdm conda --conda-cleanup-pkgs cache"
    snakemake-branch: main

- name: Create container file
  uses: snakemake/snakemake-github-action@v2
  with:
    directory: ".test"
    snakefile: "workflow/Snakefile"
    task: "containerize"