fix vcf2db: add missing dependencies #833
Workflow file for this run
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| 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 |