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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:
- dev
pull_request:
release:
types: [published]
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
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/crisprseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
ANALYSIS:
- "test_screening"
- "test_screening_paired"
- "test_screening_rra"
- "test_targeted"
- "test_umis"
- "test_screening_count_table"
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data (${{ matrix.ANALYSIS }})
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.ANALYSIS }},docker --outdir ./results_${{ matrix.ANALYSIS }}