Merge pull request #304 from JoseEspinosa/updates #70
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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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v3 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Run pipeline with test data | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |
test_controls: | |
name: Run pipeline with test data and controls | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}" | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v3 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
- name: Run pipeline with test data and controls | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_controls,docker --outdir ./results | |
parameters: | |
name: Test workflow parameters | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--skip_trimming" | |
- "--skip_merge_replicates" | |
- "--skip_consensus_peaks" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results | |
aligners: | |
name: Test available aligners | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
aligner: | |
- "bowtie2" | |
- "chromap" | |
- "star" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with the different aligners available | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }} --outdir ./results |