fix: CLIN-2414 allow to pass exomiser spring options in task.ext #291

	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:
	- main
	tags:
	- v*
	pull_request:

	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
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.10.1"
	- "latest-stable"
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v2
	with:
	version: "${{ matrix.NXF_VER }}"

	- name: Disk space cleanup
	uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

	- name: Run pipeline with test data
	# Add as many test runs as needed here. Remember that you can parallelise this by
	# using strategy.matrix.

	# Using the stub mode until our test data setup is ready
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -stub-run -profile test,docker --input "${GITHUB_WORKSPACE}/assets/TestSampleSheet.csv"

	- name: Display nextflow.log on error
	if: failure()
	run: cat .nextflow.log

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