feat: add flag to set snakemake rerun triggers (#27) #72
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| name: tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Dry_Run_and_Lint_DNA_RNA: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:latest | |
| - name: Dry Run | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:latest \ | |
| /opt2/metamorph run --input /opt2/.tests/test_cohort.txt \ | |
| --output /opt2/output --mode local --dry-run | |
| - name: View the pipeline config file [DNA & RNA modes] | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/output/config.json | |
| - name: Lint Workflow | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' | |
| Dry_Run_and_Lint_DNAonly1: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:latest | |
| - name: Dry Run [DNA only mode] | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:latest \ | |
| /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly.txt \ | |
| --output /opt2/output --mode local --dry-run | |
| - name: View the pipeline config file [DNA only mode] | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/output/config.json | |
| - name: Lint Workflow | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:latest snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' | |
| Dry_Run_DNA2: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:latest | |
| - name: Dry Run [DNA only mode w RNA column] | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:latest \ | |
| /opt2/metamorph run --input /opt2/.tests/test_cohort_DNAonly_RNAcolexists.txt \ | |
| --output /opt2/output --mode local --dry-run |