Merge pull request #67 from nf-core/use-spatialdata #225
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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: | |
branches: | |
- dev | |
- master | |
release: | |
types: [published] | |
env: | |
NXF_ANSI_LOG: false | |
CAPSULE_LOG: none | |
NFTEST_VER: "0.7.3" | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
define_nxf_versions: | |
name: Choose nextflow versions to test against depending on target branch | |
runs-on: ubuntu-latest | |
outputs: | |
matrix: ${{ steps.nxf_versions.outputs.matrix }} | |
steps: | |
- id: nxf_versions | |
run: | | |
if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | |
else | |
echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT | |
fi | |
test: | |
name: Run pipeline with test data | |
needs: define_nxf_versions | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | |
test: | |
- tests/pipeline/test_spaceranger_ffpe_v1.nf.test | |
- tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test | |
- tests/pipeline/test_downstream.nf.test | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
# Install Nextflow | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
# Install nf-test | |
- 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/ | |
# Run nf-test | |
- name: Run nf-test | |
run: nf-test test --profile=test,docker --tap=test.tap ${{ matrix.test }} | |
# If the test fails, output the software_versions.yml using the 'batcat' utility | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml |