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".": | ||
- ./.github/workflows/** | ||
- ./nf-test.config | ||
- ./nextflow.config | ||
tests: | ||
- ./assets/* | ||
- ./bin/* | ||
- ./conf/* | ||
- ./main.nf | ||
- ./nextflow_schema.json |
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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 | ||
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
on: | ||
push: | ||
branches: | ||
- "dev" | ||
- dev | ||
pull_request: | ||
branches: | ||
- "dev" | ||
- "master" | ||
release: | ||
types: | ||
- "published" | ||
types: [published] | ||
|
||
env: | ||
NXF_ANSI_LOG: false | ||
NFTEST_VER: "0.8.2" | ||
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: | ||
list: | ||
name: List Tests | ||
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | ||
outputs: | ||
# Expose matched filters as job 'modules' output variable | ||
tests: ${{ steps.list.outputs.tests }} | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
|
||
- name: Setup Nextflow | ||
uses: nf-core/setup-nextflow@v1 | ||
|
||
- name: Install nf-test | ||
if: steps.cache-software.outputs.cache-hit != 'true' | ||
run: | | ||
wget -qO- https://code.askimed.com/install/nf-test | bash | ||
sudo mv nf-test /usr/local/bin/ | ||
- name: List nf-test | ||
id: list | ||
run: | | ||
echo "tests=$(nf-test list --silent --format=json tests/pipeline/**/*.nf.test)" >> "$GITHUB_OUTPUT" | ||
test: | ||
name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) | ||
# Only run on push if this is the nf-core dev branch (merged PRs) | ||
if: needs.list.outputs.tests != '[]' | ||
needs: [list] | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
NXF_VER: | ||
- "23.04.0" | ||
- "latest-everything" | ||
profile: ["docker"] # TODO , "singularity", "conda"] | ||
test: ["${{ fromJson(needs.list.outputs.tests) }}"] | ||
shard: [1, 2, 3, 4] | ||
NXF_VER: ["latest-stable"] # TODO Test minimum version on release | ||
profile: ["docker"] | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
||
- name: Cache Nextflow installation | ||
id: cache-software | ||
uses: actions/cache@v3 | ||
with: | ||
path: | | ||
/usr/local/bin/nf-test | ||
/home/runner/.nf-test/nf-test.jar | ||
key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} | ||
fetch-depth: 0 | ||
|
||
- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v2 | ||
- uses: actions/setup-python@v4 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
|
||
- name: Disk space cleanup | ||
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
python-version: "3.11" | ||
architecture: "x64" | ||
|
||
- name: Run pipeline with test data | ||
if: steps.cache-software.outputs.cache-hit != 'true' | ||
- name: Install pdiff to see diff between nf-test snapshots | ||
run: | | ||
wget -qO- https://code.askimed.com/install/nf-test | bash | ||
sudo mv nf-test /usr/local/bin/ | ||
python -m pip install --upgrade pip | ||
pip install pdiff | ||
- name: Set up Singularity | ||
if: matrix.profile == 'singularity' | ||
uses: eWaterCycle/setup-singularity@v5 | ||
- uses: nf-core/setup-nextflow@v2 | ||
with: | ||
singularity-version: 3.7.1 | ||
version: "${{ matrix.NXF_VER }}" | ||
|
||
- name: Set up miniconda | ||
if: matrix.profile == 'conda' | ||
uses: conda-incubator/setup-miniconda@v2 | ||
- uses: nf-core/setup-nf-test@v1 | ||
with: | ||
auto-update-conda: true | ||
channels: conda-forge,bioconda,defaults | ||
python-version: ${{ matrix.python-version }} | ||
|
||
- name: Conda clean | ||
if: matrix.profile == 'conda' | ||
run: conda clean -a | ||
version: ${{ env.NFT_VER }} | ||
|
||
- name: Run nf-test | ||
- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) | ||
run: | | ||
nf-test test \ | ||
--profile="test,${{ matrix.profile }}" \ | ||
${{ matrix.test }} \ | ||
--junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml | ||
--ci \ | ||
--shard ${{ matrix.shard }}/${{ strategy.job-total }} \ | ||
--changed-until feat/workflow-updates \ | ||
--profile "+${{ matrix.profile }}" \ | ||
--filter pipeline | ||
- name: Publish Test Report | ||
uses: mikepenz/action-junit-report@v3 | ||
if: success() || failure() # run this step even if previous step failed | ||
if: always() # always run even if the previous step fails | ||
with: | ||
path: ${{ matrix.test }}-${{ matrix.profile }}.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/*/output/pipeline_info/software_versions.yml | ||
report_paths: test.xml |
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