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test(#392): Add boilerplate for tests #866

test(#392): Add boilerplate for tests

test(#392): Add boilerplate for tests #866

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:
push:
branches:
- "dev"
pull_request:
branches:
- "dev"
- "master"
release:
types:
- "published"
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.8.2"
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 }}-${{ matrix.NXF_VER }})
# Only run on push if this is the nf-core dev branch (merged PRs)
if: needs.list.outputs.tests != '[]'
needs: [list]
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile: ["docker"] # TODO , "singularity", "conda"]
test: ["${{ fromJson(needs.list.outputs.tests) }}"]
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 }}
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data
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: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
- name: Set up miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}
- name: Conda clean
if: matrix.profile == 'conda'
run: conda clean -a
- name: Run nf-test
run: |
nf-test test \
--profile="test,${{ matrix.profile }}" \
${{ matrix.test }} \
--junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: success() || failure() # run this step even if previous step failed
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