Important! Template update for nf-core/tools v3.0.2 #222
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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] | |
workflow_dispatch: | |
env: | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
NFT_VER: "0.8.4" | |
NFT_WORKDIR: "~" | |
NXF_ANSI_LOG: false | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
nf-test-changes: | |
name: Check for changes | |
runs-on: ubuntu-latest | |
outputs: | |
nf_test_files: ${{ steps.list.outputs.nf_test_files }} | |
steps: | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Install Python dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install gitpython pyyaml | |
- name: list nf_test_files | |
id: list | |
run: | | |
echo nf_test_files=$(python \ | |
.github/python/find_changed_files.py \ | |
-t pipeline workflow process \ | |
--head_ref ${{ github.sha }} \ | |
--base_ref origin/${{ github.base_ref }} \ | |
) >> $GITHUB_OUTPUT | |
- name: debug | |
run: | | |
echo ${{ steps.list.outputs.nf_test_files }} | |
test: | |
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.nf_test_files }} | ${{ matrix.profile }})" | |
needs: [nf-test-changes] | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/riboseq') && needs.nf-test-changes.outputs.nf_test_files != '[]')}}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
profile: | |
- "conda" | |
- "docker" | |
- "singularity" | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
# Exclude conda and singularity on dev | |
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
exclude: | |
- isMaster: false | |
profile: "conda" | |
- isMaster: false | |
profile: "singularity" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Set up nf-test | |
uses: nf-core/setup-nf-test@v1 | |
with: | |
version: ${{ env.NFT_VER }} | |
- name: Set up Apptainer | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-apptainer@main | |
- name: Set up Singularity | |
if: matrix.profile == 'singularity' | |
run: | | |
mkdir -p $NXF_SINGULARITY_CACHEDIR | |
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
- name: Cache pdiff | |
uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
id: cache-pip-pdiff | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-pdiff | |
- name: Set up pdiff to see diff between nf-test snapshots | |
run: | | |
python -m pip install --upgrade pip | |
pip install pdiff cryptography | |
- name: Set up Miniconda | |
if: matrix.profile == 'conda' | |
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
with: | |
miniconda-version: "latest" | |
auto-update-conda: true | |
conda-solver: libmamba | |
channels: conda-forge,bioconda | |
- name: Set up Conda | |
if: matrix.profile == 'conda' | |
run: | | |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
echo $(realpath python) >> $GITHUB_PATH | |
- name: Disk space cleanup | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Run nf-test | |
run: | | |
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap | |
- uses: pcolby/tap-summary@v1 | |
with: | |
path: >- | |
test.tap | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: test.xml | |
confirm-pass: | |
runs-on: ubuntu-latest | |
needs: [test] | |
if: always() | |
steps: | |
- name: All tests ok | |
if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
run: exit 0 | |
- name: One or more tests failed | |
if: ${{ contains(needs.*.result, 'failure') }} | |
run: exit 1 | |
- name: debug-print | |
if: always() | |
run: | | |
echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |