test user override with env variable #14

	name: Nextflow Test Pipeline Container

	on:
	push:
	branches: [ main, dev ]
	pull_request:
	branches: [ main ]
	workflow_dispatch:

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Setup Java
	uses: actions/setup-java@v4
	with:
	distribution: 'temurin'
	java-version: '17'

	- name: Cache Docker images
	uses: actions/cache@v4
	with:
	path: /tmp/.buildx-cache
	key: docker-cache-${{ runner.os }}-${{ hashFiles('/nextflow.config', '/modules.config') }}
	restore-keys: \|
	docker-cache-${{ runner.os }}-

	- name: Capture runner UID/GID
	run: \|
	echo "UID=$(id -u)" >> $GITHUB_ENV
	echo "GID=$(id -g)" >> $GITHUB_ENV

	- name: Install Nextflow
	run: \|
	curl -s https://get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/
	nextflow -version

	- name: Run Nextflow pipeline with Docker
	env:
	NXF_DEFAULT_DOCKER_OPTS: "-u ${{ env.UID }}:${{ env.GID }}"
	run: \|
	nextflow run main.nf -profile test -with-docker

	- name: Check test completion and details
	run: \|
	# Check if the test.passed file was created
	if [ ! -f "results/test/test.passed" ]; then
	echo "ERROR: Test completion file 'results/test/test.passed' not found"
	echo "Test pipeline did not complete successfully"
	exit 1
	fi

	echo "✅ Test completed successfully!"

	- name: Upload test results
	uses: actions/upload-artifact@v4
	if: always()
	with:
	name: nextflow-test-results
	path: \|
	results/
	.nextflow.log
	retention-days: 7

Provide feedback