refactor: Change how quast and recombination inputs work #651

	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:
	- master
	pull_request:
	release:
	types: [published]

	env:
	NXF_ANSI_LOG: false

	jobs:
	test-stub:
	name: Run pipeline with stubs
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'beiko-lab/arete') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "latest-stable"
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@v2

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

	- name: Run pipeline stub-run
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub-run --outdir ./stub_results

	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 == 'beiko-lab/arete') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	profile: ["docker", "singularity"]
	NXF_VER:
	- "latest-stable"
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@v2

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

	- name: Set up Singularity
	if: matrix.profile == 'singularity'
	uses: eWaterCycle/setup-singularity@v5
	with:
	singularity-version: 3.7.1

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

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