Important! Template update for nf-core/tools v3.0.2 #1376
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
name: nf-core CI | |
on: | |
push: | |
branches: | |
- "dev" | |
pull_request: | |
branches: | |
- "dev" | |
- "master" | |
release: | |
types: [published] | |
workflow_dispatch: | |
env: | |
NXF_ANSI_LOG: false | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
NFTEST_VER: "0.9.0" | |
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", "23.10.0"]' | tee -a $GITHUB_OUTPUT | |
fi | |
test: | |
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
profile: | |
- "conda" | |
- "docker" | |
- "singularity" | |
test_name: | |
- "test" | |
- "test_nothing" | |
- "test_bakta" | |
- "test_prokka" | |
- "test_bgc_pyrodigal" | |
- "test_bgc_bakta" | |
- "test_bgc_prokka" | |
- "test_taxonomy_pyrodigal" | |
- "test_taxonomy_bakta" | |
- "test_taxonomy_prokka" | |
- "test_preannotated" | |
- "test_preannotated_bgc" | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
# Exclude conda and singularity on dev | |
exclude: | |
- isMaster: false | |
profile: "conda" | |
- isMaster: false | |
profile: "singularity" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Check out test data | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: funcscan | |
path: test-datasets/ | |
fetch-depth: 1 | |
- 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: 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: Clean up Disk space | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- 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/ | |
- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | |
run: | | |
nf-test test --tag ${{ matrix.test_name }} --profile ${{ matrix.test_name }},${{ matrix.profile }} --junitxml=test.xml | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/*/tests/output/pipeline_info/software_versions.yml | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: "*.xml" |