Implement #260: Implement a basic CI test-run pipeline in Github Actions #18

	name: CI
	# This workflow runs the pipeline with the minimal test dataset to check that
	# it completes without any syntax errors
	on:
	push:
	branches:
	- dev
	- 260-improve-ci
	pull_request:
	release:
	types: [published]

	env:
	NXF_ANSI_LOG: false

	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 in the main repository
	if: "${{ github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/jasen' }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.10.1"
	parameters:
	- "-profile staphylococcus_aureus"
	#- "-profile mycobacterium_tuberculosis"
	#- "-profile klebsiella_pneumoniae"
	#- "-profile escherichia_coli"
	steps:
	- name: Install Nextflow
	# For running (locally) with ACT, we use a docker image with Nextflow pre-installed
	if: "${{ ! github.event.act }}"
	uses: nf-core/setup-nextflow@v1
	with:
	version: "${{ matrix.NXF_VER }}"

	- name: Check out pipeline code
	uses: actions/checkout@v3

	- name: Activate minimal version of cgMLST database
	run: \|
	'mv assets/cgmlst{,_orig} && ln -sr assets/cgmlst{_minimal,}'

	- name: Install containers
	run:
	'cd container && sudo make build_local_containers && make download_remote_containers'

	- name: Run Make install
	run:
	'make install'

	- name: Run pipeline with test data
	run: \|
	nextflow run ${GITHUB_WORKSPACE}/main.nf ${{ matrix.parameters }} -config configs/nextflow.ci.config --csv assets/test_data/samplelist.testrun.csv

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