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Merge pull request #354 from nf-core/fix-linting #993

Merge pull request #354 from nf-core/fix-linting

Merge pull request #354 from nf-core/fix-linting #993

Workflow file for this run

# 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:
release:
types: [published]
merge_group:
types:
- checks_requested
branches:
- master
- dev
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.8.1"
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile: ["alevin", "cellranger", "cellrangermulti", "kallisto", "star"]
steps:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- 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.NFTEST_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 nf-test
run: |
nf-test test tests/main_pipeline_${{ matrix.profile }}.test --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/*/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