Add bam input #227
This file contains hidden or 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: Run nf-test | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "**/meta.yml" | |
| - "**/*.md" | |
| - "**/*.png" | |
| - "**/*.svg" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| # 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" | |
| NFT_VER: "0.9.2" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| jobs: | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test-changes | |
| - runner=4cpu-linux-x64 | |
| 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: 14 | |
| - name: debug | |
| run: | | |
| echo ${{ steps.set-shards.outputs.shard }} | |
| echo ${{ steps.set-shards.outputs.total_shards }} | |
| nf-test: | |
| name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" | |
| needs: [nf-test-changes] | |
| if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-nf-test | |
| - runner=4cpu-linux-x64 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} | |
| profile: [conda, docker, singularity] | |
| isMain: | |
| - ${{ github.base_ref == 'master' || github.base_ref == 'main' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMain: false | |
| profile: "conda" | |
| - isMain: false | |
| profile: "singularity" | |
| NXF_VER: | |
| - "24.10.5" | |
| - "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 | |
| id: run_nf_test | |
| uses: ./.github/actions/nf-test | |
| continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} | |
| env: | |
| 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 }} | |
| - name: Report test status | |
| if: ${{ always() }} | |
| run: | | |
| if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then | |
| echo "::error::Test with ${{ matrix.NXF_VER }} failed" | |
| # Add to workflow summary | |
| echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY | |
| if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then | |
| echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." | |
| fi | |
| if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
| exit 1 | |
| fi | |
| fi | |
| confirm-pass: | |
| needs: [nf-test] | |
| if: always() | |
| runs-on: # use self-hosted runners | |
| - runs-on=${{ github.run_id }}-confirm-pass | |
| - runner=2cpu-linux-x64 | |
| steps: | |
| - name: One or more tests failed (excluding latest-everything) | |
| 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::" |