Skip to content

Merge pull request #142 from maxulysse/fix_dbsnp_known_indels_usage #323

Merge pull request #142 from maxulysse/fix_dbsnp_known_indels_usage

Merge pull request #142 from maxulysse/fix_dbsnp_known_indels_usage #323

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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnavar') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
test:
- "default"
- "annotation"
- "removeduplicates"
- "skipbasecalib"
- "bamcsiindex"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: 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: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes