Add CI to build mulled containers with Wave #4080
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| name: Wave | ||
| # When environment.yml is changed | ||
| on: | ||
| pull_request: | ||
| paths: | ||
| - "**/environment.yml" | ||
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| env: | ||
| WAVE_VER: "1.4.1" | ||
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| jobs: | ||
| gen-matrix: | ||
| name: generate-matrix | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | ||
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| - 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" | ||
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| outputs: | ||
| matrix: ${{ steps.set-matrix.outputs.matrix }} | ||
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| build: | ||
| if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}" | ||
| needs: gen-matrix | ||
| name: build | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 60 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}" | ||
| steps: | ||
| - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | ||
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| - name: Install wave-cli | ||
| run: | | ||
| wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${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 | ||
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| - name: Create a registry name | ||
| uses: actions/github-script@v7 | ||
| id: registry-name | ||
| with: | ||
| result-encoding: string | ||
| script: | | ||
| return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/environment.yml', '').replace('/', '_'); | ||
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| - name: Build container | ||
| if: matrix.profile == 'docker' | ||
| run: | | ||
| wave --conda-file "${{ matrix.files }}" \ | ||
| --freeze \ | ||
| --await \ | ||
| --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \ | ||
| --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} | ||
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| - name: Build Singularity | ||
| if: matrix.profile == 'singularity' | ||
| run: | | ||
| wave --conda-file "${{ matrix.files }}" \ | ||
| --freeze \ | ||
| --await \ | ||
| --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \ | ||
| --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \ | ||
| --singularity | ||
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| # TODO Build from Dockerfiles | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| # renovate: datasource=conda depName=bioconda/bowtie | ||
| - bioconda::bowtie=1.3.1 | ||
| # renovate: datasource=conda depName=bioconda/samtools | ||
| - bioconda::samtools=1.20 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| # renovate: datasource=conda depName=bioconda/bowtie | ||
| - bioconda::bowtie=1.3.1 | ||
| # renovate: datasource=conda depName=bioconda/samtools | ||
| - bioconda::samtools=1.20 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| # renovate: datasource=conda depName=bioconda/htslib | ||
| - bioconda::htslib=1.20 | ||
| # renovate: datasource=conda depName=bioconda/samtools | ||
| - bioconda::samtools=1.20 |
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This is to have
namein the conda environment, right? We can remove if so.There was a problem hiding this comment.
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No, this was to have a different wave repo per module. We can keep this for anything built by a Dockerfile for now(bclconvert, cellranger, etc.)