move gatk preprocessing to sbwf #86
Workflow file for this run
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| name: Run nf-test | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| pull_request: | |
| branches: [dev] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "ubuntu-latest" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFT_VER: "0.9.2" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| jobs: | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| outputs: | |
| shard: ${{ steps.set-shards.outputs.shard }} | |
| total_shards: ${{ steps.set-shards.outputs.total_shards }} | |
| steps: | |
| - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: get number of shards | |
| id: set-shards | |
| uses: ./.github/actions/get-shards | |
| env: | |
| NFT_VER: ${{ env.NFT_VER }} | |
| with: | |
| max_shards: 7 | |
| - name: debug | |
| run: | | |
| echo ${{ steps.set-shards.outputs.shard }} | |
| echo ${{ steps.set-shards.outputs.total_shards }} | |
| nf-test: | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" | |
| needs: [nf-test-changes] | |
| if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} | |
| profile: [conda, docker, singularity] | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| NXF_VER: | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| - "24.10.2" | |
| - "latest-everything" | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test | |
| uses: ./.github/actions/nf-test | |
| env: | |
| NFT_DIFF: ${{ env.NFT_DIFF }} | |
| NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} | |
| NFT_WORKDIR: ${{ env.NFT_WORKDIR }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| with: | |
| profile: ${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| confirm-pass: | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| needs: [nf-test] | |
| if: always() | |
| steps: | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: One or more tests cancelled | |
| if: ${{ contains(needs.*.result, 'cancelled') }} | |
| run: exit 1 | |
| - name: All tests ok | |
| if: ${{ contains(needs.*.result, 'success') }} | |
| run: exit 0 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "::group::DEBUG: `needs` Contents" | |
| echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | |
| echo "::endgroup::" | |
| - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner | |
| if: always() | |
| run: | | |
| ls -la ./ | |
| rm -rf ./* || true | |
| rm -rf ./.??* || true | |
| ls -la ./ |