kallisto|bustools 0.28.2 update #817
Workflow file for this run
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
name: nf-core CI | |
on: | |
push: | |
branches: | |
- dev | |
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: | |
name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}" | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
profile: ["alevin", "cellranger", "kallisto", "star"] | |
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 tests/main_pipeline_${{ matrix.profile }}.test --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 |