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Merge pull request #163 #418

Merge pull request #163

Merge pull request #163 #418

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
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:
test:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
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
with:
fetch-depth: 0
# - name: Set up JDK 11
# uses: actions/setup-java@v2
# with:
# java-version: "11"
# distribution: "adopt"
- uses: actions/setup-python@v4
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/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
run: |
nf-test test \
--ci \
--shard ${{ matrix.shard }}/${{ strategy.job-total }} \
--changed-since HEAD^ \
--profile "+${{ matrix.profile }}" \
--filter pipeline
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: test.xml