feat: add group-by-variant-oncoprint #1411
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name: Tests | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches_ignore: [] | |
jobs: | |
Formatting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
# Full git history is needed to get a proper | |
# list of changed files within `super-linter` | |
fetch-depth: 0 | |
- name: Formatting | |
uses: github/super-linter@v4 | |
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@v2 | |
- name: Lint workflow | |
uses: snakemake/snakemake-github-action@v1.24.0 | |
with: | |
directory: . | |
snakefile: workflow/Snakefile | |
stagein: "mamba install -y -n snakemake --channel conda-forge pyarrow=6.0" | |
args: "--lint" | |
Testing: | |
runs-on: ubuntu-latest | |
needs: | |
- Linting | |
- Formatting | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Test workflow (local FASTQs) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
- name: Test testcase generation | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "results/testcases/a/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
- name: Test report | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-simple/config.yaml --report report.zip" | |
- name: Test workflow (local FASTQs, target regions) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
stagein: | | |
rm -rf .test/results | |
- name: Test workflow (local FASTQs, multiple target regions BED files) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
stagein: | | |
rm -rf .test/results | |
- name: Test workflow (local FASTQs, no candidate filtering) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-no-candidate-filtering/config.yaml --dryrun --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
stagein: | | |
rm -rf .test/results | |
- name: Test workflow (local FASTQs primer) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
stagein: | | |
rm -rf .test/results | |
- name: Test workflow (SRA FASTQs) | |
uses: snakemake/snakemake-github-action@v1 | |
with: | |
directory: .test | |
snakefile: workflow/Snakefile | |
args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda -n -j 10 --conda-cleanup-pkgs cache" | |
stagein: | | |
rm -rf .test/results |