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Important! Template update for nf-core/tools v2.13.1 #144

Important! Template update for nf-core/tools v2.13.1

Important! Template update for nf-core/tools v2.13.1 #144

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:
pull_request:
release:
types: [published]
merge_group:
types:
- checks_requested
branches:
- master
- dev
env:
NXF_ANSI_LOG: false
NFT_VER: "0.8.3"
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:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'tags' output variable
tags: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v3
- name: Combine all tags.yml files
id: get_username
run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
- name: debug
run: cat .github/tags.yml
- uses: dorny/paths-filter@v2
id: filter
with:
filters: ".github/tags.yml"
define_nxf_versions:
name: Choose nextflow versions to test against depending on target branch
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.nxf_versions.outputs.matrix }}
steps:
- id: nxf_versions
run: |
if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
else
echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
fi
test:
name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
needs: [changes, define_nxf_versions]
if: needs.changes.outputs.tags != '[]'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
profile:
- "docker"
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Cache nf-test installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
- 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: Run pipeline with test data
# TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nf-test test --verbose --tag ${{ matrix.tags }} --profile test,"${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
- 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