Fix module section linter regex #7312
Workflow file for this run
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name: Create a pipeline and test it | |
on: | |
push: | |
branches: | |
- dev | |
paths-ignore: | |
- "docs/**" | |
- "CHANGELOG.md" | |
pull_request: | |
paths-ignore: | |
- "docs/**" | |
- "CHANGELOG.md" | |
release: | |
types: [published] | |
workflow_dispatch: | |
inputs: | |
runners: | |
description: "Runners to test on" | |
type: choice | |
options: | |
- "ubuntu-latest" | |
- "self-hosted" | |
default: "self-hosted" | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
env: | |
NXF_ANSI_LOG: false | |
jobs: | |
RunTestWorkflow: | |
# use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default | |
runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
env: | |
NXF_ANSI_LOG: false | |
strategy: | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
steps: | |
- name: go to working directory | |
run: | | |
mkdir -p create-test-wf | |
cd create-test-wf | |
export NXF_WORK=$(pwd) | |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
name: Check out source-code repository | |
- name: Set up Python 3.12 | |
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
with: | |
python-version: "3.12" | |
- name: Install python dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install . | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: ${{ matrix.NXF_VER }} | |
- name: Run nf-core/tools | |
run: | | |
mkdir create-test-wf && cd create-test-wf | |
export NXF_WORK=$(pwd) | |
nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" | |
nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results | |
- name: Upload log file artifact | |
if: ${{ always() }} | |
uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
with: | |
name: nf-core-log-file-${{ matrix.NXF_VER }} | |
path: create-test-wf/log.txt | |
- name: Cleanup work directory | |
# cleanup work directory | |
run: sudo rm -rf create-test-wf | |
if: always() |