Important! Template update for nf-core/tools v3.0.1 #334
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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 --width 120 --expand-tabs=2" | |
NFT_VER: "0.9.0" | |
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: | |
test: | |
runs-on: ubuntu-latest | |
name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5" | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
filter: ["workflow", "function", "pipeline"] | |
# filter: ["process", "workflow", "function", "pipeline"] | |
profile: ["conda", "docker", "singularity"] | |
shard: [1, 2, 3, 4] | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
exclude: | |
- isMaster: false | |
profile: "conda" | |
- isMaster: false | |
profile: "singularity" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ 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/[email protected] | |
- name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5" | |
run: | | |
nf-test test \ | |
--ci \ | |
--debug \ | |
--verbose \ | |
--junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
--shard ${{ matrix.shard }}/5 \ | |
--changed-since HEAD^ \ | |
--follow-dependencies \ | |
--profile "+${{ matrix.profile }}" \ | |
--filter ${{ matrix.filter }} | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v4 | |
if: success() || failure() # always run even if the previous step fails | |
with: | |
report_paths: "TEST-*.xml" | |
- name: Clean up | |
if: always() | |
run: | | |
sudo rm -rf /home/ubuntu/tests/ |