riasc is testing ScanNeo2 #345
Workflow file for this run
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name: Linting | |
run-name: ${{ github.actor }} is testing ScanNeo2 | |
on: [push] | |
jobs: | |
formatting: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout with submodules | |
uses: actions/checkout@v3 | |
with: | |
submodules: recursive | |
fetch-depth: 1 | |
- name: Formatting | |
uses: github/super-linter@v5 | |
env: | |
VALIDATE_ALL_CODEBASE: false | |
DEFAULT_BRANCH: master | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
linting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- run: pwd | |
- uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: '.tests' | |
snakefile: 'workflow/Snakefile' | |
args: '--lint --configfile .tests/integration/config_basic/config.yaml' | |
#run-workflow: | |
#runs-on: ubuntu-latest | |
#needs: | |
#- linting | |
#- formatting | |
#steps: | |
#- name: Checkout repository with submodules | |
#uses: actions/checkout@v3 | |
#with: | |
#submodules: recursive | |
#- name: Test workflow (basic model, no batch_effects) | |
#uses: snakemake/[email protected] | |
#with: | |
#directory: .test | |
#snakefile: workflow/Snakefile | |
#args: "--configfile .test/config_basic/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
#- name: Test report (basic model, no batch_effects) | |
#uses: snakemake/[email protected] | |
#with: | |
#directory: .test | |
#snakefile: workflow/Snakefile | |
#args: "--configfile .test/config_basic/config.yaml --report report.zip" | |
#- name: Test workflow (multiple variables_of_interest, include batch_effects) | |
#uses: snakemake/[email protected] | |
#with: | |
#directory: .test | |
#snakefile: workflow/Snakefile | |
#args: "--configfile .test/config_complex/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
#- name: Test report (multiple variables_of_interest, include batch_effects) | |
#uses: snakemake/[email protected] | |
#with: | |
#directory: .test | |
#snakefile: workflow/Snakefile | |
#args: "--configfile .test/config_complex/config.yaml --report report.zip"b |