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Integrated nf-test into pipeline CI #49

Integrated nf-test into pipeline CI

Integrated nf-test into pipeline CI #49

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
pull_request:
env:
NXF_ANSI_LOG: false
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:
nf-test-changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
nf_test_files: ${{ steps.list.outputs.components }}
steps:
- uses: actions/[email protected]
with:
fetch-depth: 0
- name: List nf-test files
id: list
uses: adamrtalbot/[email protected]
with:
head: ${{ github.sha }}
base: origin/${{ github.base_ref }}
include: .github/include.yaml
- name: print list of nf-test files
run: |
echo ${{ steps.list.outputs.components }}
test:
name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
needs: [nf-test-changes]
if: needs.nf-test-changes.outputs.nf_test_files != '[]'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "24.04.2"
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
profile:
- "docker"
steps:
- name: Check out pipeline code
uses: actions/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- uses: actions/[email protected]
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/[email protected]
with:
version: 0.9.0
- name: Disk space cleanup
if: matrix.nf_test_files == 'tests/stub/main.nf.test'
uses: jlumbroso/[email protected]
- name: Run nf-test
run: |
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}"
confirm-pass:
runs-on: ubuntu-latest
needs: [test]
if: always()
steps:
- name: All tests ok
if: ${{ !contains(needs.*.result, 'failure') }}
run: exit 0
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1
- name: debug-print
if: always()
run: |
echo "toJSON(needs) = ${{ toJSON(needs) }}"
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"