PINTS Updates #966
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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@bab30c2299617f6615ec02a68b9a40d10bd21366 # v45 | |
| with: | |
| json: true | |
| escape_json: false | |
| files: | | |
| modules/**/environment.yml | |
| - name: Find Dockerfile differences | |
| id: docker-diff | |
| uses: tj-actions/changed-files@bab30c2299617f6615ec02a68b9a40d10bd21366 # 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 "[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 |