Run Synteny Test #1

	name: Run Synteny Test

	on:
	workflow_dispatch

	env:
	NEXTFLOW_VERSION: 23.10.1
	NF_TEST_VERSION: 0.8.3

	jobs:

	build:

	runs-on: ubuntu-latest

	steps:
	- name: Clean workspace before start
	run: rm -rf $GITHUB_WORKSPACE/*

	- uses: actions/[email protected]

	- name: Set up JDK 11
	uses: actions/[email protected]
	with:
	java-version: '11'
	distribution: 'adopt'

	- name: Install nextflow
	run: sudo bash; cd /opt; wget "https://github.com/nextflow-io/nextflow/releases/download/v${NEXTFLOW_VERSION}/nextflow"; chmod +x nextflow;

	- name: Install nf-test
	run: sudo bash; cd /opt; wget "https://github.com/askimed/nf-test/releases/download/v${NF_TEST_VERSION}/nf-test-${NF_TEST_VERSION}.tar.gz"; tar -xvf "nf-test-${NF_TEST_VERSION}.tar.gz"; chmod +x nf-test; rm "/opt/nf-test-${NF_TEST_VERSION}.tar.gz"

	- name: Add software to path
	run: echo "/opt" >> $GITHUB_PATH;

	- name: download test data
	run: cd data/synteny_input; wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1wfrcvTd264dvp-tmq_6vDqo95S-7oIAs' -O Drosophila_santomea.cds; wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1NuaL5vWiV2-L08PJpKGNxFk1gYemOKaA' -O Drosophila_simulans.cds

	- name: Run synteny test
	run: nf-test test tests/modules/synteny.nf.test

	- name: Clean workspace after finish
	run: rm -rf $GITHUB_WORKSPACE/*

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