Added SEQKIT_RMDUP to detect duplicate sequence and wrap the fasta to… #32

	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

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

	jobs:
	test:
	name: Run pipeline with test data
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'Plant-Food-Research-Open/genepal') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.04.0"
	TEST_PARAMS:
	- minimal
	- short
	- nonmasked
	- stub
	OPTION_STUB:
	- "-stub"

	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
	run: \|
	nextflow run \
	${GITHUB_WORKSPACE} \
	-profile docker \
	-params-file \
	./tests/${{ matrix.TEST_PARAMS }}/params.json \
	${{ matrix.OPTION_STUB }} \
	--outdir ./results \
	--max_cpus 2 \
	--max_memory '6.GB' \
	--max_time '2.h'

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