Merge pull request #7 from buschlab/cram #20
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| name: Docker Image CI | |
| on: | |
| push: | |
| jobs: | |
| build: | |
| if: github.repository == 'buschlab/bam-matcher' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Cache Reference Genome | |
| id: cache-reference | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/work/bam-matcher/reference | |
| key: reference | |
| - name: Download-Reference | |
| if: steps.cache-reference.outputs.cache-hit != 'true' | |
| run: sudo apt-get update && sudo apt-get install -y tabix samtools && mkdir /home/runner/work/bam-matcher/reference && wget https://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz -O /home/runner/work/bam-matcher/reference/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz && bgzip -d /home/runner/work/bam-matcher/reference/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz && samtools faidx /home/runner/work/bam-matcher/reference/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa && samtools dict /home/runner/work/bam-matcher/reference/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa > /home/runner/work/bam-matcher/reference/Homo_sapiens.GRCh37.75.dna.primary_assembly.dict | |
| - name: Build the Docker image | |
| run: docker build . --file Dockerfile --tag ghcr.io/buschlab/bam-matcher:latest --label maintainer="Niklas Reimer <n.reimer@uni-luebeck.de>" | |
| - name: Test VarScan | |
| run: docker run --rm -v /home/runner/work/bam-matcher/reference:/ref:ro -v $(pwd)/test_data/ci.conf:/bam-matcher/ci.conf:ro -v $(pwd):/output ghcr.io/buschlab/bam-matcher:latest --bam1 test_data/sample1.bam --bam2 test_data/sample2.bam --config ci.conf -so --output /output/varscan.txt --caller varscan | |
| - name: Verify VarScan | |
| run: cmp -s varscan.txt test_data/varscan.txt | |
| - name: Test GATK4 | |
| run: docker run --rm -v /home/runner/work/bam-matcher/reference:/ref:ro -v $(pwd)/test_data/ci.conf:/bam-matcher/ci.conf:ro -v $(pwd):/output ghcr.io/buschlab/bam-matcher:latest --bam1 test_data/sample1.bam --bam2 test_data/sample2.bam --config ci.conf -so --output /output/gatk4.txt --caller gatk4 | |
| - name: Verify GATK4 | |
| run: cmp -s gatk4.txt test_data/gatk4.txt | |
| - name: Test Freebayes | |
| run: docker run --rm -v /home/runner/work/bam-matcher/reference:/ref:ro -v $(pwd)/test_data/ci.conf:/bam-matcher/ci.conf:ro -v $(pwd):/output ghcr.io/buschlab/bam-matcher:latest --bam1 test_data/sample1.bam --bam2 test_data/sample2.bam --config ci.conf -so --output /output/freebayes.txt --caller freebayes | |
| - name: Verify Freebayes | |
| run: cmp -s freebayes.txt test_data/freebayes.txt | |
| - name: Login to Docker registry | |
| uses: docker/login-action@v3 | |
| if: github.ref == 'refs/heads/py3' | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Upload Docker image | |
| if: github.ref == 'refs/heads/py3' | |
| run: docker push ghcr.io/buschlab/bam-matcher:latest |