Fix/readme 391 #919
Workflow file for this run
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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 | |
NFT_VER: "0.9.0" | |
NFT_WORKDIR: "~" | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
shard: [1, 2, 3, 4, 5] | |
NXF_VER: ["latest-stable"] # TODO Test minimum version on release | |
profile: ["docker"] | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- name: Install pdiff to see diff between nf-test snapshots | |
run: | | |
python -m pip install --upgrade pip | |
pip install pdiff | |
- uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- uses: nf-core/setup-nf-test@v1 | |
with: | |
version: ${{ env.NFT_VER }} | |
- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) | |
run: | | |
nf-test test \ | |
--ci \ | |
--shard ${{ matrix.shard }}/${{ strategy.job-total }} \ | |
--changed-since HEAD^ \ | |
--profile "+${{ matrix.profile }}" | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: test.xml |