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Merge pull request #119 from nf-core/dev
v2.0 Release Candidate
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -15,7 +15,7 @@ jobs: | |
| test: | ||
| name: Run standard pipeline test | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}" | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| NXF_VER: ${{ matrix.nxf_ver }} | ||
|
|
@@ -26,9 +26,9 @@ jobs: | |
| # Nextflow versions | ||
| include: | ||
| # Test pipeline minimum Nextflow version | ||
| - NXF_VER: '21.10.3' | ||
| - NXF_VER: "21.10.3" | ||
| # Test latest nextflow version | ||
| - NXF_VER: '' | ||
| - NXF_VER: "" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
@@ -39,7 +39,7 @@ jobs: | |
| 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 pipelie execution | ||
| # 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 | ||
|
|
@@ -49,9 +49,11 @@ jobs: | |
| 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 | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | ||
| - name: Run Pipeline | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | ||
| attempt_limit: 2 | ||
|
|
||
| ############################## | ||
| ### LARGE INTEGRATION TEST ### | ||
|
|
@@ -68,7 +70,7 @@ jobs: | |
| strategy: | ||
| matrix: | ||
| # Nextflow versions: check pipeline minimum and current latest | ||
| nxf_ver: ['21.10.3', ''] | ||
| nxf_ver: ["21.10.3", ""] | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
@@ -79,7 +81,7 @@ jobs: | |
| 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 pipelie execution | ||
| # 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 | ||
|
|
@@ -89,9 +91,11 @@ jobs: | |
| 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 with test data | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip | ||
| - name: Run Pipeline | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip | ||
| attempt_limit: 2 | ||
|
|
||
| ##################################### | ||
| ### EDGE VERSION INTEGRATION TEST ### | ||
|
|
@@ -102,7 +106,7 @@ jobs: | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }} | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| NXF_VER: '' | ||
| NXF_VER: "" | ||
| NXF_EDGE: 1 | ||
| NXF_ANSI_LOG: false | ||
| CAPSULE_LOG: none | ||
|
|
@@ -117,7 +121,7 @@ jobs: | |
| nextflow self-update | ||
| # Work around for the unexpected end of file error that github actions seems to get when downloading compressed | ||
| # files during pipelie execution | ||
| # 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 | ||
|
|
@@ -127,9 +131,11 @@ jobs: | |
| 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 with test data | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | ||
| - name: Run Pipeline | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip | ||
| attempt_limit: 2 | ||
|
|
||
| ############################## | ||
| ### UNIT TESTS ### | ||
|
|
@@ -144,45 +150,87 @@ jobs: | |
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| nxf_version: ['21.10.3', ''] | ||
| tags: ["samplesheet", "verify_output_input", "verify_output_align_short", "verify_output_align_long", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"] | ||
| nxf_version: ["21.10.3", ""] | ||
| tags: | ||
| - test_params | ||
| - test_samplesheet | ||
| - verify_output_save_ref | ||
| - verify_output_only_input | ||
| - verify_output_save_merged | ||
| - verify_output_skip_fastqc | ||
| - verify_output_save_trimmed | ||
| - verify_output_skip_trimming | ||
| - verify_output_align_intermed | ||
| - verify_output_align_only_align | ||
| - verify_output_align_save_spikein_align | ||
| - verify_output_align_save_unaligned | ||
| - verify_output_only_filtering | ||
| - verify_output_align_duplicates_mark | ||
| - verify_output_align_duplicates_remove | ||
| - verify_output_align_duplicates_remove_target | ||
| - verify_output_peak_calling_only_peak_calling | ||
| - 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_conseneus_peaks_group | ||
| - test_conseneus_peaks_all | ||
| - test_conseneus_peaks_invalid | ||
| - verify_output_reporting_skip_reporting | ||
| - verify_output_reporting_skip_igv | ||
| - verify_output_reporting_skip_heatmaps | ||
| - verify_output_reporting_skip_multiqc | ||
| - verify_output_skip_frip | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Checkout Code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: "3.x" | ||
|
|
||
| - uses: actions/cache@v2 | ||
| - name: Setup Pip Cache | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ~/.cache/pip | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: "3.x" | ||
| - name: Install Python dependencies | ||
| run: python -m pip install --upgrade pip pytest-workflow | ||
|
|
||
| - uses: actions/cache@v2 | ||
| - name: Restore Keys | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: /usr/local/bin/nextflow | ||
| key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-nextflow- | ||
| - name: Install Nextflow | ||
| env: | ||
| NXF_VER: ${{ matrix.nxf_version }} | ||
| CAPSULE_LOG: none | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| - name: Run pytest-workflow | ||
| run: pytest --tag ${{ matrix.tags }} --kwdof | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: pytest --tag ${{ matrix.tags }} --kwdof | ||
| attempt_limit: 3 | ||
|
|
||
| - name: Upload logs on failure | ||
| if: failure() | ||
|
|
||
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