wave.yml

name: Wave
# When environment.yml is changed
on:
  pull_request:
    paths:
      - "**/environment.yml"
      - "**/Dockerfile"

# TODO On complete call testing CI
# TODO Skip testing CI if any changes to environment.yml

env:
  # renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
  WAVE_VERSION: "1.5.0"
  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
  NFT_VER: "0.9.2"
  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
  NXF_VER: "24.10.1"

jobs:
  generate-matrix:
    name: generate-matrix
    runs-on: ubuntu-latest
    # Only run on Pull Requests within the same repository, and not from forks
    if: github.event.pull_request.head.repo.full_name == github.repository
    outputs:
      conda-matrix: ${{ steps.conda-diff.outputs.all_changed_files }}
      dockerfile-matrix: ${{ steps.docker-diff.outputs.all_changed_files }}
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Find conda differences
        id: conda-diff
        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
        with:
          json: true
          escape_json: false
          files: |
            modules/**/environment.yml

      - name: Find Dockerfile differences
        id: docker-diff
        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
        with:
          json: true
          escape_json: false
          files: |
            modules/**/Dockerfile

  conda-wave:
    # NOTE This should get skipped because generate-matrix won't run
    # if: github.repository == 'nf-core/modules'
    if: ${{ needs.generate-matrix.outputs.conda-matrix != '[]' }}
    needs: generate-matrix
    name: Build ${{ matrix.profile }} ${{ matrix.platform }} Container
    runs-on: ubuntu-latest
    timeout-minutes: 60
    strategy:
      fail-fast: false
      max-parallel: 4
      matrix:
        files: "${{ fromJson(needs.generate-matrix.outputs.conda-matrix) }}"
        profile: [docker, singularity]
        platform: ["linux/amd64", "linux/arm64"]
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Install wave-cli
        run: |
          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
          chmod +x /usr/local/bin/wave

      - name: Build ${{ matrix.profile }} container
        # FIXME Hack while iron out the CI
        continue-on-error: true
        env:
          PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
        run: |
          wave --conda-file "${{ matrix.files }}" \
              $PROFILE \
              --freeze \
              --await \
              --platform ${{ matrix.platform }} \
              --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}

  dockerfile-wave:
    # NOTE This should get skipped because generate-matrix won't run
    # if: github.repository == 'nf-core/modules'
    if: ${{ needs.generate-matrix.outputs.dockerfile-matrix != '[]' }}
    needs: generate-matrix
    name: Build Dockerfile-based ${{ matrix.platform }} Container
    runs-on: ubuntu-latest
    timeout-minutes: 60
    strategy:
      fail-fast: false
      max-parallel: 4
      matrix:
        files: "${{ fromJson(needs.generate-matrix.outputs.dockerfile-matrix) }}"
        # NOTE singularity build requires a Singularity definition file in place of Dockerfile
        # https://nextflow.slack.com/archives/C0477AS31T5/p1731755350230149?thread_ts=1731697852.661849&cid=C0477AS31T5
        # profile: [docker]
        platform: ["linux/amd64", "linux/arm64"]
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Install wave-cli
        run: |
          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
          chmod +x /usr/local/bin/wave

      - name: Create a registry name
        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
        id: registry-name
        with:
          result-encoding: string
          script: |
            return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/Dockerfile', '').replace('/', '_');

      - name: Build ${{ matrix.platform }} container
        # NOTE If you're changing a Dockerfile and this is running, try to update the Dockerfile to build with wave
        continue-on-error: false
        run: |
          wave -f "${{ matrix.files }}" \
              --freeze \
              --await \
              --platform ${{ matrix.platform }} \
              --build-repo quay.io/nf-core/modules/${{steps.registry-name.outputs.result}} \
              --cache-repository quay.io/nf-core/wave-cache/docker/${{ matrix.platform }} \
              --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}

  # bump-versions:
  #   needs: generate-matrix
  #   name: bump-versions
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
  #       with:
  #         distribution: "temurin"
  #         java-version: "17"

  #     - uses: nf-core/setup-nextflow@v2

  #     - uses: nf-core/setup-nf-test@v1
  #       with:
  #         version: ${{ env.NFT_VER }}

  #     - name: Bump Snapshot Versions
  #       env:
  #         # NFT_DIFF: "pdiff"
  #         # NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
  #         SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
  #         SENTIEON_AUTH_MECH: "GitHub Actions - token"
  #       run: |
  #         # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
  #         if [ "${{ matrix.profile }}" == "docker" ]; then
  #           PROFILE="docker_self_hosted"
  #         else
  #           PROFILE=${{ matrix.profile }}
  #         fi

  #         NFT_WORKDIR=~ \
  #         nf-test test \
  #           --profile=${{ matrix.profile }} \
  #           --tap=test.tap \
  #           # --ci \
  #           --verbose \
  #           --only-changed \
  #           # --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \
  #           # --filter ${{ matrix.filter }} \
  #           --follow-dependencies \
  #           --tag version \
  #           --update-snapshot

  #     - name: Commit & push version bumps
  #       run: |
  #         git config user.email "core@nf-co.re"
  #         git config user.name "nf-core-bot"
  #         git config push.default upstream
  #         git add .
  #         git status
  #         git commit -m "[automated] Bump versions snapshot"
  #         git push