checkout actions update #2
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name: Tests | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches_ignore: [] | |
jobs: | |
formatting: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout with submodules | |
uses: actions/[email protected] | |
with: | |
submodules: recursive | |
fetch-depth: 0 | |
- name: Formatting | |
uses: github/super-linter@v5 | |
env: | |
VALIDATE_ALL_CODEBASE: false | |
DEFAULT_BRANCH: main | |
VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
linting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/[email protected] | |
- name: Linting | |
uses: snakemake/[email protected] | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--lint" | |
run-workflow: | |
runs-on: ubuntu-latest | |
needs: | |
- linting | |
- formatting | |
steps: | |
- name: Checkout repository with submodules | |
uses: actions/[email protected] | |
with: | |
submodules: recursive | |
- name: Test workflow | |
uses: snakemake/[email protected] | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
# - name: Test report | |
# uses: snakemake/[email protected] | |
# with: | |
# directory: .test | |
# snakefile: workflow/Snakefile | |
# args: "--use-conda --use-singularity --cores 2 --report report.zip" |