feat: Handle trimmed fastqs plus additional fixes (#252) #621
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| name: Benchmark | |
| #on: | |
| # push: | |
| # branches: [ master ] | |
| # pull_request: | |
| # branches: [ master ] | |
| # TODO enable | |
| # on: | |
| # schedule: | |
| # - cron: 0 13 * * 1 # every monday at 1PM UTC | |
| jobs: | |
| benchmark-giab: | |
| name: Benchmark GIAB exome | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v2 | |
| - name: Download benchmark | |
| id: benchmark_download | |
| uses: compsci-commons/qc-benchmark-action@main | |
| with: | |
| task: download | |
| benchmark_name: giab-na12878-exome | |
| - name: Write config | |
| env: | |
| DATA: ${{ steps.benchmark_download.outputs.data }} | |
| run: | | |
| # Read location: $DATA/reads.1.fq and $DATA/reads.2.fq | |
| # Reference genome: $DATA/reference.fa | |
| echo -e "NA12878\t1\t../$DATA/reads.1.fq\t../$DATA/reads.2.fq\t\t-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" >> .test/config-giab/units.tsv | |
| - name: Cache workflow results | |
| id: cache-results | |
| uses: actions/cache@v2 | |
| with: | |
| path: .test/results/final-calls/NA12878.present.fdr-controlled.vcf.gz | |
| key: key-${{ hashFiles('workflow/**') }}-${{ hashFiles('.test/config-giab/**') }} | |
| - name: Run workflow | |
| uses: snakemake/[email protected] | |
| if: steps.cache-results.outputs.cache-hit != 'true' | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "results/final-calls/NA12878.present.fdr-controlled.vcf.gz results/final-calls/NA12878.annotated.bcf --configfile .test/config-giab/config.yaml --use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp" | |
| - name: Eval benchmark | |
| uses: compsci-commons/qc-benchmark-action@main | |
| id: benchmark_eval | |
| with: | |
| task: eval | |
| benchmark_name: giab-na12878-exome | |
| results-path: .test/results/final-calls/NA12878.present.fdr-controlled.vcf.gz | |
| - name: Show results | |
| env: | |
| REPORT: ${{ steps.benchmark_eval.outputs.report }} | |
| run: | | |
| cat $REPORT.summary.csv | |
| - name: Upload all calls as artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: benchmark-all-calls | |
| path: .test/results/final-calls/NA12878.annotated.bcf | |
| - name: Upload filtered calls as artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: benchmark-filtered-calls | |
| path: .test/results/final-calls/NA12878.present.fdr-controlled.vcf.gz | |
| - name: Upload report as artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: benchmark-report | |
| path: ${{ steps.benchmark_eval.outputs.report }}.* |