Add CI to build mulled containers with Wave #114
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| 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 | |
| - 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 "[email protected]" | |
| 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 | |
| # TODO Build from Dockerfiles |