Trio #439

	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
	NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
	NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
	SINGULARITY_DISABLE_CACHE: true

	concurrency:
	group: "${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}"
	cancel-in-progress: true

	jobs:
	test:
	name: Run pipeline with test data
	# Only run on push if this is the nf-core dev branch (merged PRs)
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'sanger-tol/genomeassembly') }}"
	runs-on: ubuntu2204-4c
	strategy:
	matrix:
	NXF_VER:
	- "22.10.1"
	- "latest-everything"
	steps:
	- name: Login to GitHub Container Registry
	uses: docker/login-action@v3
	with:
	registry: ghcr.io
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}
	- name: Check out pipeline code
	uses: actions/checkout@v3

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1
	with:
	version: "${{ matrix.NXF_VER }}"

	- name: Set up nextflow secrets
	run: \|
	nextflow secrets set NCBI_API_KEY ${{ secrets.NCBI_API_KEY }}

	- name: Setup apptainer
	uses: eWaterCycle/setup-apptainer@main

	- name: Set up Singularity
	run: \|
	mkdir -p $NXF_SINGULARITY_CACHEDIR
	mkdir -p $NXF_SINGULARITY_LIBRARYDIR

	- name: Run pipeline with test data
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results

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