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Important! Template update for nf-core/tools v2.9 #210

Important! Template update for nf-core/tools v2.9

Important! Template update for nf-core/tools v2.9 #210

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:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnavar') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
test:
- "default"
- "annotation"
- "removeduplicates"
- "skipbasecalib"
- "bamcsiindex"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
- name: Run pipeline with tests settings
run: pytest --tag ${{matrix.test}} --kwdof