Add skeleton for samplesheet generation #99
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# 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 | |
NFTEST_VER: "0.7.3" | |
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: | |
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 $GITHUB_OUTPUT | |
fi | |
test: | |
name: nf-test | |
needs: define_nxf_versions | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/createtaxdb') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
profile: | |
- "conda" | |
- "docker" | |
- "singularity" | |
test_name: | |
- "test" | |
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: Set up Apptainer | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-apptainer@main | |
- name: Check out test data | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: createtaxdb | |
path: test-datasets/ | |
fetch-depth: 1 | |
- 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 nf-test | |
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" |