wave.yml

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

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

env:
  WAVE_VER: "1.5.0"
  NFTEST_VER: "0.9.1"

jobs:
  gen-matrix:
    name: generate-matrix
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4

      - name: Calculate file differences
        id: diff
        uses: tj-actions/changed-files@v44
        with:
          json: true
          quotepath: false
          # TODO Add Dockerfiles
          files: |
            modules/**/environment.yml
      - name: Debug
        run: echo ${{ steps.diff.outputs.all_changed_files }}
      - id: set-matrix
        run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"

    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}

  build:
    if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
    needs: gen-matrix
    name: build
    runs-on: ubuntu-latest
    timeout-minutes: 60
    strategy:
      fail-fast: false
      matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
    steps:
      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4

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

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

      - name: Build container
        if: matrix.profile == 'docker'
        run: |
          wave --conda-file "${{ matrix.files }}" \
              --freeze \
              --await \
              --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}

      - name: Build Singularity
        if: matrix.profile == 'singularity'
        run: |
          wave --conda-file "${{ matrix.files }}" \
              --freeze \
              --await \
              --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
              --singularity

    # TODO Build from Dockerfiles

  # bump-versions:
  #   needs: gen-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.NFTEST_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