updated parameters for allele schema #515
Workflow file for this run
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name: Pipeline 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 phac-nml dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/mikrokondo') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Cache nf-test installation | |
id: cache-software | |
uses: actions/cache@v3 | |
with: | |
path: | | |
/usr/local/bin/nf-test | |
/home/runner/.nf-test/nf-test.jar | |
key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest | |
- name: Install nf-test | |
if: steps.cache-software.outputs.cache-hit != 'true' | |
run: | | |
wget -qO- https://code.askimed.com/install/nf-test | bash | |
sudo mv nf-test /usr/local/bin/ | |
- name: Disk space cleanup | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Run nf-test | |
run: | | |
nf-test test | |
- name: Nextflow run with test profile | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |