diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5d28ca0..d80035c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -25,7 +25,7 @@ jobs: steps: - uses: actions/checkout@v2 - name: Lint workflow - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: . snakefile: workflow/Snakefile @@ -40,15 +40,15 @@ jobs: - uses: actions/checkout@v2 - name: Test workflow - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: .test snakefile: workflow/Snakefile - args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" + args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp" - name: Test report - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: .test snakefile: workflow/Snakefile - args: "--report report.zip" \ No newline at end of file + args: "--report report.zip" diff --git a/workflow/Snakefile b/workflow/Snakefile index 7ddaaa0..46dc637 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,11 +1,15 @@ -# Main entrypoint of the workflow. -# Please follow the best practices: +# Main entrypoint of the workflow. +# Please follow the best practices: # https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html, -# in particular regarding the standardized folder structure mentioned there. +# in particular regarding the standardized folder structure mentioned there. + rule touch: - output: "file.txt" - conda: "../envs/empty.yaml" - log: "logs/touch.log" + output: + "file.txt", + conda: + "envs/empty.yaml" + log: + "logs/touch.log", shell: "touch {output}"