benchmark-giab.yml

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/snakemake-github-action@v1.22.0
        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 }}.*