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create-test-lint-wf-template.yml
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name: Create a pipeline from a template and test it
on:
push:
branches:
- dev
paths:
- nf_core/pipeline-template/**
pull_request:
paths-ignore:
- "docs/**"
- "CHANGELOG.md"
release:
types: [published]
workflow_dispatch:
inputs:
runners:
description: "Runners to test on"
type: choice
options:
- "ubuntu-latest"
- "self-hosted"
default: "self-hosted"
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
env:
NXF_ANSI_LOG: false
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
jobs:
prepare-matrix:
name: Retrieve all template features
runs-on: ubuntu-latest
outputs:
all_features: ${{ steps.create_matrix.outputs.matrix }}
steps:
- name: 🏗 Set up yq
uses: frenck/action-setup-yq@v1
- name: checkout
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Create Matrix
id: create_matrix
run: |
echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
RunTestWorkflow:
runs-on: ${{ matrix.runner }}
needs: prepare-matrix
env:
NXF_ANSI_LOG: false
strategy:
matrix:
TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
runner:
# use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
- ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
profile: ["self_hosted_runner"]
include:
- TEMPLATE: all
runner: ubuntu-latest
profile: "docker"
- TEMPLATE: nf_core_configs
runner: ubuntu-latest
profile: "docker"
exclude:
- TEMPLATE: nf_core_configs
profile: "self_hosted_runner"
fail-fast: false
steps:
- name: go to working directory
run: |
mkdir -p create-lint-wf-template
cd create-lint-wf-template
export NXF_WORK=$(pwd)
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
name: Check out source-code repository
- name: Set up Python 3.12
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.12"
- name: Install python dependencies
run: |
python -m pip install --upgrade pip
pip install .
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: latest-everything
# Create template files
- name: Create template skip ${{ matrix.TEMPLATE }}
run: |
mkdir create-test-lint-wf
export NXF_WORK=$(pwd)
if [ ${{ matrix.TEMPLATE }} == "all" ]
then
printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml
else
printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml
fi
# Create a pipeline from the template
- name: create a pipeline from the template ${{ matrix.TEMPLATE }}
run: |
cd create-test-lint-wf
nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml
- name: run the pipeline
run: |
cd create-test-lint-wf
nextflow run my-prefix-testpipeline -profile test,${{matrix.profile}} --outdir ./results
# Remove results folder before linting
- name: remove results folder
run: |
rm -rf create-test-lint-wf/results
# Try syncing it before we change anything
- name: nf-core pipelines sync
run: nf-core --log-file log.txt pipelines sync --dir create-test-lint-wf/my-prefix-testpipeline/
# Run code style linting
- name: Run pre-commit
run: pre-commit run --all-files
working-directory: create-test-lint-wf
# Remove TODO statements
- name: remove TODO
run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
working-directory: create-test-lint-wf
# Uncomment includeConfig statement
- name: uncomment include config
run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
working-directory: create-test-lint-wf
# Replace zenodo.XXXXXX to pass readme linting
- name: replace zenodo.XXXXXX
run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
working-directory: create-test-lint-wf
# Run nf-core linting
- name: nf-core pipelines lint
run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned
working-directory: create-test-lint-wf
# Run bump-version
- name: nf-core pipelines bump-version
run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1
working-directory: create-test-lint-wf
# Run nf-core linting in release mode
- name: nf-core pipelines lint in release mode
run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned --release
working-directory: create-test-lint-wf
- name: Tar files
run: tar -cvf artifact_files.tar log.txt template_skip*.yml
working-directory: create-test-lint-wf
- name: Upload log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
with:
name: nf-core-log-file-${{ matrix.TEMPLATE }}
path: create-test-lint-wf/artifact_files.tar
- name: Cleanup work directory
run: sudo rm -rf create-test-lint-wf
if: always()