Updates #37
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| name: nf-test | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.7.3" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| nf_test: | |
| name: nf-test tests | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/clipseq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "22.10.1" | |
| - "latest-everything" | |
| profile: ["docker"] | |
| test: ["test"] | |
| tag: | |
| - "genome_no_chrom_sizes" | |
| - "genome_fasta_raw" | |
| - "genome_fasta_gz" | |
| - "genome_fasta_fai" | |
| - "genome_ncrna_fasta_gz" | |
| - "genome_ncrna_fasta" | |
| - "genome_ncrna_fasta_fai" | |
| - "genome_gtf_raw" | |
| - "genome_gtf_gz" | |
| - "genome_gtf_filt" | |
| - "genome_gtf_filt_seg" | |
| - "genome_gtf_seg" | |
| - "genome_gtf_resolve_unanno" | |
| - "genome_gtf_resolve_unanno_region" | |
| - "genome_gtf_resolve_unanno_genic" | |
| - "genome_gtf_resolve_unanno_region_genic" | |
| - "genome_star_build_index" | |
| - "genome_bt_build_index" | |
| - "genome_no_longest_transcript" | |
| - "genome_preset" | |
| - "only_input_primary" | |
| - "only_preprocessing_primary" | |
| - "only_preprocessing_skip_fastqc" | |
| - "only_preprocessing_skip_umi_extract" | |
| - "only_preprocessing_skip_trimming" | |
| - "only_alignment_primary" | |
| - "only_alignment_false_outputs" | |
| - "only_filtering_primary" | |
| - "only_filtering_false_outputs" | |
| - "only_dedup_primary" | |
| - "only_crosslinking_primary" | |
| - "only_peakcalling_primary" | |
| - "only_peakcalling_caller_param_fail" | |
| - "only_peakcalling_clippy" | |
| - "only_peakcalling_icount" | |
| - "only_peakcalling_paraclu" | |
| - "only_peakcalling_paraclu_clippy" | |
| include: | |
| - test: test_full_small | |
| profile: docker | |
| tag: "full_small_only_input_primary" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| run: nf-test test --profile=${{ matrix.test }},${{ matrix.profile }} --tap=test.tap --tag ${{ matrix.tag }} tests/nf_test/${{ matrix.test }}/*.test | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap |