Important! Template update for nf-core/tools v2.13.1 #144
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: | |
pull_request: | |
release: | |
types: [published] | |
merge_group: | |
types: | |
- checks_requested | |
branches: | |
- master | |
- dev | |
env: | |
NXF_ANSI_LOG: false | |
NFT_VER: "0.8.3" | |
NFT_WORKDIR: "~" | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
changes: | |
name: Check for changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'tags' output variable | |
tags: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Combine all tags.yml files | |
id: get_username | |
run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
- name: debug | |
run: cat .github/tags.yml | |
- uses: dorny/paths-filter@v2 | |
id: filter | |
with: | |
filters: ".github/tags.yml" | |
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: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
needs: [changes, define_nxf_versions] | |
if: needs.changes.outputs.tags != '[]' | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | |
tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | |
profile: | |
- "docker" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Disk space cleanup | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Cache nf-test installation | |
id: cache-software | |
uses: actions/cache@v3 | |
with: | |
path: | | |
/usr/local/bin/nf-test | |
/home/runner/.nf-test/nf-test.jar | |
key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest | |
- name: Install nf-test | |
if: steps.cache-software.outputs.cache-hit != 'true' | |
run: | | |
wget -qO- https://code.askimed.com/install/nf-test | bash | |
sudo mv nf-test /usr/local/bin/ | |
- name: Run pipeline with test data | |
# TODO nf-core: You can customise CI pipeline run tests as required | |
# For example: adding multiple test runs with different parameters | |
# Remember that you can parallelise this by using strategy.matrix | |
run: | | |
nf-test test --verbose --tag ${{ matrix.tags }} --profile test,"${{ 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 |