Skip to content

Merging-template-3.0.1 #687

Merging-template-3.0.1

Merging-template-3.0.1 #687

Workflow file for this run

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]
workflow_dispatch:
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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data (docker)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
- name: Run pipeline with test data (singularity)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
if: "${{ github.base_ref == 'master' }}"
- name: Run pipeline with test data (conda)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
if: "${{ github.base_ref == 'master' }}"
parameters:
name: Test workflow parameters
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
parameters:
- "--skip_trimming"
- "--skip_consensus_peaks"
- "--aligner bowtie2"
- "--aligner chromap"
- "--aligner star"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with various parameters (docker)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
- name: Run pipeline with various parameters (singularity)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results ${{ matrix.parameters }}
if: "${{ github.base_ref == 'master' }}"
- name: Run pipeline with various parameters (conda)
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results ${{ matrix.parameters }}
if: "${{ github.base_ref == 'master' }}"