Personal-Genome-Pipeline/.github/workflows/container-test.yml at main · GeiserX/Personal-Genome-Pipeline · GitHub

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name: Container Smoke Test

on:
  push:
    branches: [main]
    paths: ['versions.env', 'scripts/setup.sh', '.github/workflows/container-test.yml']
  pull_request:
    branches: [main]
    paths: ['versions.env', 'scripts/setup.sh', '.github/workflows/container-test.yml']
  workflow_dispatch:
  schedule:
    # Monthly check that upstream images are still pullable
    - cron: '0 6 1 * *'

permissions:
  contents: read

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  pull-and-verify:
    runs-on: [self-hosted, linux, x64]
    strategy:
      fail-fast: false
      matrix:
        include:
          # Representative subset — one per registry/publisher to catch auth/rename issues
          - image: staphb/bcftools:1.21
            cmd: "bcftools --version"
          - image: quay.io/biocontainers/minimap2:2.28--he4a0461_0
            cmd: "minimap2 --version"
          - image: brentp/duphold:v0.2.3
            cmd: "duphold --version"
          - image: getwilds/annotsv:3.4.4
            cmd: "AnnotSV --version"
          - image: broadinstitute/picard:3.4.0
            cmd: "java -version"
          - image: pgkb/pharmcat:3.2.0
            cmd: "pharmcat_pipeline --version"
          - image: python:3.11
            cmd: "python3 --version"
          - image: quay.io/biocontainers/vcfanno:0.3.7--he881be0_0
            cmd: "bash -c 'vcfanno 2>&1 | grep -q \"vcfanno version\"'"
          # slivar uses staphb/bcftools + pre-built binary (no dedicated container)
          - image: quay.io/biocontainers/pypgx:0.26.0--pyh7e72e81_0
            cmd: "pypgx --version"
    steps:
      - name: Pull ${{ matrix.image }}
        run: docker pull "${{ matrix.image }}"

      - name: Verify ${{ matrix.image }}
        run: docker run --rm "${{ matrix.image }}" ${{ matrix.cmd }}

  versions-env-sync:
    runs-on: [self-hosted, linux, x64]
    steps:
      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4

      - name: Verify smoke-test matrix matches versions.env
        run: |
          echo "Checking that container-test matrix images exist in versions.env..."
          rm -f /tmp/matrix_fail

          # Extract only "- image: <value>" lines from the YAML matrix block
          # These always start with leading whitespace, a dash, and "image:"
          grep -E '^\s+- image:' .github/workflows/container-test.yml | awk '{print $3}' | while read -r img; do
            if ! grep -qF "$img" versions.env; then
              echo "FAIL: container-test.yml matrix has $img but it's not in versions.env"
              echo "1" > /tmp/matrix_fail
            fi
          done

          if [ -f /tmp/matrix_fail ]; then
            exit 1
          fi
          echo "OK: All matrix images exist in versions.env"