Pipeline restructure #18

	name: run-pipeline

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main
	workflow_dispatch:

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository with LFS
	uses: actions/checkout@v3
	with:
	lfs: true

	- name: Check if Dockerfile has changed
	run: \|
	if git diff --name-only ${{ github.event.before }} ${{ github.sha }} \| grep 'Dockerfile'; then
	echo "DOCKERFILE_CHANGED=true" >> $GITHUB_ENV
	else
	echo "DOCKERFILE_CHANGED=false" >> $GITHUB_ENV
	fi

	- name: Docker Login (for pull or push)
	run: \|
	echo "${{ secrets.DOCKER_PASSWORD }}" \| docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin

	- name: Build Docker image (if changed)
	if: env.DOCKERFILE_CHANGED == 'true'
	run: \|
	docker build -t eppicenter/mad4hatter:latest .

	- name: Pull Docker image (if not built)
	if: env.DOCKERFILE_CHANGED == 'false'
	run: \|
	docker pull eppicenter/mad4hatter:latest

	- name: Setup Nextflow
	uses: nf-core/setup-nextflow@v1

	- name: Run Nextflow Pipeline (Docker)
	run: \|
	nextflow -q run main.nf --readDIR ${GITHUB_WORKSPACE}/data/testdata --target v4 -profile test,docker --genome v1 -c conf/test.config

	- name: Archive Work Directory
	if: failure() # Only archive if the workflow failed
	run: \|
	tar -czf work-dir.tar.gz /home/runner/work/mad4hatter/mad4hatter

	- name: Upload Work Directory
	if: failure() # Only upload if the workflow failed
	uses: actions/upload-artifact@v2
	with:
	name: work-dir
	path: work-dir.tar.gz

	- name: Push Docker image (if built)
	if: env.DOCKERFILE_CHANGED == 'true'
	run: \|
	docker push eppicenter/mad4hatter:latest

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