This action runs Snakemake on the repository.
Required The working directory to use. Default .test.
The Snakefile containing the workflow description. Default Snakefile.
Additional arguments to pass to Snakemake.
Preliminary commands to run before the workflow execution.
Whether to run Snakemake or to generate a container image specification (Dockerfile, apptainer.def) that contains all required environments. Can be either run or containerize. Default run.
Whether used disk space shall be printed if Snakemake fails. Can be either true or false (default: false).
Snakemake version to install from conda. Default * (latest available version from the configured channels).
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.
Whether to install Apptainer (true/false). Default false.
Additional arguments for containerize, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile).
- 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" containerize-args: "apptainer"