Updates #571
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| ############################## | |
| ### SMALL INTEGRATION TEST ### | |
| ############################## | |
| test: | |
| name: Run standard pipeline test | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}" | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| strategy: | |
| matrix: | |
| NXF_VER: ["23.04.0", ""] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| # Work around for the unexpected end of file error that github actions seems to get when downloading compressed | |
| # files during pipeline execution | |
| - name: Download data | |
| run: | | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz | |
| - name: Run Pipeline | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | |
| attempt_limit: 2 | |
| ############################## | |
| ### LARGE INTEGRATION TEST ### | |
| ############################## | |
| test_full_small: | |
| name: Run extended pipeline test | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| NXF_VER: ["23.04.0", ""] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| # Work around for the unexpected end of file error that github actions seems to get when downloading compressed | |
| # files during pipeline execution | |
| - name: Download data | |
| run: | | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz | |
| - name: Run Pipeline | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip | |
| attempt_limit: 2 | |
| ##################################### | |
| ### EDGE VERSION INTEGRATION TEST ### | |
| ##################################### | |
| test_edge: | |
| name: Run standard pipeline test (edge version) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "latest-everything" | |
| # Work around for the unexpected end of file error that github actions seems to get when downloading compressed | |
| # files during pipeline execution | |
| - name: Download data | |
| run: | | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz | |
| wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz | |
| - name: Run Pipeline | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | |
| attempt_limit: 2 | |
| ############################## | |
| ### UNIT TESTS ### | |
| ############################## | |
| unit_tests: | |
| name: ${{ matrix.NXF_VER }} ${{ matrix.tags }} | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} | |
| runs-on: ubuntu-20.04 | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: ["23.04.0", ""] | |
| tags: | |
| - test_genome_options | |
| - test_genome_options_spikein | |
| - test_samplesheet | |
| - test_samplesheet_2 | |
| - test_samplesheet_3 | |
| - test_filtering_noqfilter | |
| - test_filtering_withqfilter | |
| - test_bam_scale_none | |
| - test_bam_scale_spikein | |
| - test_bam_scale_cpm | |
| - test_bam_scale_rpkm | |
| - test_bam_scale_bpm | |
| - test_bam_scale_cpm_iggscale | |
| - test_peak_callers_seacr | |
| - test_peak_callers_macs2 | |
| - test_peak_callers_invalid | |
| - test_peak_callers_seacr_macs2 | |
| - test_peak_callers_macs2_seacr | |
| - test_peak_callers_seacr_macs2_noigg | |
| - test_peak_callers_ctrl_tests | |
| - test_consensus_peaks_group | |
| - test_consensus_peaks_all | |
| - test_consensus_peaks_invalid | |
| - verify_output_only_input | |
| - verify_output_save_merged | |
| - verify_output_save_trimmed | |
| - verify_output_skip_trimming | |
| - verify_output_skip_fastqc | |
| - verify_output_save_ref | |
| - verify_output_align_only_align | |
| - verify_output_align_only_align_end_to_end | |
| - verify_output_align_only_align_local | |
| - verify_output_align_intermed | |
| - verify_output_align_save_spikein_align | |
| - verify_output_align_save_unaligned | |
| - verify_output_align_duplicates_mark | |
| - verify_output_align_duplicates_remove | |
| - verify_output_align_duplicates_remove_target | |
| - verify_output_align_linear_duplicates_remove | |
| - verify_output_align_linear_duplicates_remove_target | |
| - verify_output_only_filtering | |
| - verify_output_only_filtering_with_mitochondrial_reads | |
| - verify_output_only_filtering_without_mitochondrial_reads | |
| - verify_output_only_filtering_without_mitochondrial_reads_mito_name_null | |
| - verify_output_peak_calling_only_peak_calling | |
| - verify_output_reporting_skip_preseq_false | |
| - verify_output_reporting_skip_preseq_true | |
| - verify_output_reporting_skip_dtqc_false | |
| - verify_output_reporting_skip_dtqc_true | |
| - verify_output_reporting_skip_heatmaps_false | |
| - verify_output_reporting_skip_heatmaps_true | |
| - verify_output_reporting_skip_heatmaps_grouped | |
| - verify_output_reporting_skip_igv_false | |
| - verify_output_reporting_skip_igv_true | |
| - verify_output_reporting_skip_multiqc_false | |
| - verify_output_reporting_skip_multiqc_true | |
| - verify_output_reporting_skip_peak_qc_false | |
| - verify_output_reporting_skip_peak_qc_true | |
| - verify_output_reporting_skip_reporting | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.x" | |
| - name: Setup Pip Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow | |
| - name: Restore Keys | |
| uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pytest-workflow | |
| uses: Wandalen/wretry.action@v1.0.11 | |
| with: | |
| command: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.tags }} --symlink --kwdof --color=yes | |
| attempt_limit: 3 | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: logs-unit-tests | |
| path: | | |
| /home/runner/pytest_workflow_*/*/.nextflow.log | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/work | |
| !/home/runner/pytest_workflow_*/*/work/conda | |
| !/home/runner/pytest_workflow_*/*/work/singularity |