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ci.yml
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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:
push:
branches:
- main
tags:
- v*
pull_request:
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.10.1"
- "latest-stable"
steps:
- 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: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data
# Add as many test runs as needed here. Remember that you can parallelise this by
# using strategy.matrix.
# Using the stub mode until our test data setup is ready
run: |
nextflow run ${GITHUB_WORKSPACE} -stub-run -profile test,docker --input "${GITHUB_WORKSPACE}/assets/TestSampleSheet.csv"
- name: Display nextflow.log on error
if: failure()
run: cat .nextflow.log