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Nf-test

Nf-test #770

Workflow file for this run

# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
pull_request:
release:
types: [published]
merge_group:
types:
- checks_requested
branches:
- master
- dev
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.8.1"
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:

Check failure on line 23 in .github/workflows/ci.yml

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The workflow is not valid. .github/workflows/ci.yml (Line: 23, Col: 3): The workflow must contain at least one job with no dependencies.
name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
needs: [changes, define_nxf_versions]
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile:
[
"tests/main_pipeline_alevin.test",
"tests/main_pipeline_cellranger.test",
"tests/main_pipeline_kallisto.test",
"tests/main_pipeline_star.test",
]
steps:
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Check out pipeline code
uses: actions/checkout@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: Run nf-test
run: |
nf-test test "${{ matrix.profile }}" --junitxml=test.xml
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
- 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