3.2.1 Release Candidiate #562
This file contains 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: 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 |