Update vcf2maf and add stub tests #3869
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: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # 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 }} | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFT_VER: "0.9.2" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| NXF_VER: "24.10.2" | |
| jobs: | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose detected tags as 'modules' and 'workflows' output variables | |
| paths: ${{ steps.list.outputs.components }} | |
| modules: ${{ steps.outputs.outputs.modules }} | |
| subworkflows: ${{ steps.outputs.outputs.subworkflows}} | |
| # Prod for version bumping | |
| 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: List nf-test files | |
| id: list | |
| uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6 | |
| with: | |
| head: ${{ github.sha }} | |
| base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }} | |
| n_parents: 0 | |
| exclude_tags: "gpu" | |
| - name: Separate modules and subworkflows | |
| id: outputs | |
| run: | | |
| echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT | |
| echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT | |
| - name: debug | |
| run: | | |
| echo ${{ steps.list.outputs.components }} | |
| echo ${{ steps.outputs.outputs.modules }} | |
| echo ${{ steps.outputs.outputs.subworkflows }} | |
| nf-test: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| name: "${{ matrix.profile }} | ${{ matrix.shard }}" | |
| needs: nf-test-changes | |
| if: ${{ needs.nf-test-changes.outputs.modules != '[]' || needs.nf-test-changes.outputs.subworkflows != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: [1, 2, 3, 4, 5] | |
| profile: [conda, docker_self_hosted, singularity] | |
| env: | |
| NXF_ANSI_LOG: false | |
| TOTAL_SHARDS: 5 | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| env: | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| with: | |
| profile: ${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| paths: "${{ join(fromJson(needs.nf-test-changes.outputs.paths), ' ') }}" | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| 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 "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |