Add umicollapse as an alternative to umi-tools #3181
Workflow file for this run
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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: | |
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: | |
nf-test-changes: | |
name: Check for changes | |
runs-on: ubuntu-latest | |
outputs: | |
nf_test_files: ${{ steps.list.outputs.components }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: List nf-test files | |
id: list | |
uses: adamrtalbot/[email protected] | |
with: | |
head: ${{ github.sha }} | |
base: origin/${{ github.base_ref }} | |
include: .github/include.yaml | |
- name: print list of nf-test files | |
run: | | |
echo ${{ steps.list.outputs.components }} | |
test: | |
name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" | |
needs: [nf-test-changes] | |
if: needs.nf-test-changes.outputs.nf_test_files != '[]' | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
profile: | |
- "docker" | |
- "singularity" | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
# Exclude conda and singularity on dev | |
exclude: | |
- isMaster: false | |
profile: "singularity" | |
- NXF_VER: "latest-everything" | |
profile: "singularity" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 | |
with: | |
distribution: "temurin" | |
java-version: "17" | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Set up Apptainer | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-apptainer@main | |
- name: Set up Singularity | |
if: matrix.profile == 'singularity' | |
run: | | |
mkdir -p $NXF_SINGULARITY_CACHEDIR | |
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
- name: Install nf-test | |
uses: nf-core/setup-nf-test@v1 | |
with: | |
version: ${{ env.NFT_VER }} | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- name: Install pdiff to see diff between nf-test snapshots | |
run: | | |
python -m pip install --upgrade pip | |
pip install pdiff | |
- name: Clean up Disk space | |
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: ${{ !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) }}" |