foundry/.github/workflows/verification-workflows.yml at main · galaxyproject/foundry · GitHub

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name: Verification workflows

on:
  pull_request:
    paths:
      - "verification/workflows/**"
      - ".github/workflows/verification-workflows.yml"
  push:
    branches: [main]
    paths:
      - "verification/workflows/**"
      - ".github/workflows/verification-workflows.yml"

jobs:
  planemo:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: false
          channels: conda-forge,bioconda
          channel-priority: strict

      - name: Install Planemo
        run: python -m pip install planemo==0.75.41

      - name: Lint verified workflow
        continue-on-error: true
        shell: bash
        run: |
          set -euo pipefail
          planemo --version
          command -v planemo
          mapfile -t workflows < <(git ls-files 'verification/workflows/**/*.gxwf.yml')
          if [ "${#workflows[@]}" -eq 0 ]; then
            echo "No verification workflows found" >&2
            exit 1
          fi
          for workflow in "${workflows[@]}"; do
            planemo lint "$workflow"
          done

      - name: Test verified workflow
        shell: bash
        run: |
          set -euo pipefail
          mkdir -p upload
          mapfile -t workflows < <(git ls-files 'verification/workflows/**/*.gxwf.yml')
          if [ "${#workflows[@]}" -eq 0 ]; then
            echo "No verification workflows found" >&2
            exit 1
          fi
          for workflow in "${workflows[@]}"; do
            name="${workflow#verification/workflows/}"
            name="${name//\//-}"
            name="${name%.gxwf.yml}"
            planemo test "$workflow" \
              --galaxy_branch release_25.1 \
              --test_output_json "upload/${name}.json" \
              --test_output "upload/${name}.html" \
              --summary minimal
          done

      - uses: actions/upload-artifact@v4
        if: always()
        with:
          name: verification-workflows-planemo
          path: upload/