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main.yml
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name: Tests
on:
push:
branches:
- master
pull_request:
branches_ignore: []
jobs:
formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout with submodules
uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- 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
- name: Linting
uses: snakemake/[email protected]
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_complex/config.yaml --lint"
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"