Ben made me do this #790
Workflow file for this run
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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] | |
env: | |
NXF_ANSI_LOG: false | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test_all: | |
name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }} | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/germline') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "24.04.0" | |
- "latest-everything" | |
test: | |
- "pipeline_default" | |
- "pipeline_callers" | |
- "pipeline_variations" | |
- "pipeline_variations2" | |
- "pipeline_gvcfs" | |
- "cram_call_genotype_gatk4" | |
- "cram_call_vardictjava" | |
- "cram_prepare_samtools_bedtools" | |
- "input_split_bedtools" | |
- "vcf_annotation" | |
- "vcf_extract_relate_somalier" | |
- "vcf_ped_rtgtools" | |
- "vcf_upd_updio" | |
- "vcf_validate_small_variants" | |
steps: | |
- name: Free some space | |
run: | | |
sudo rm -rf /usr/share/dotnet | |
sudo rm -rf /opt/ghc | |
sudo rm -rf "/usr/local/share/boost" | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Disk space cleanup | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Install nf-test | |
run: | | |
conda install -c bioconda nf-test | |
- name: Run pipeline with test data | |
run: | | |
$CONDA/bin/nf-test test --tag ${{ matrix.test }} --junitxml=default.xml | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: "default.xml" | |
- name: Upload log file artifact | |
if: failure() | |
uses: actions/upload-artifact@v3 | |
with: | |
name: nf-test-workdir | |
path: .nf-test/ |