updated timeseries test #18

	name: Nextflow CI

	on:
	push:
	branches:
	- development
	pull_request:
	branches:
	- master

	jobs:
	test_sarscov2_user:
	name: Run pipeline test (user)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Install Nextflow
	run: \|
	wget -qO- get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Run pipeline test (user)
	run: \|
	nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml

	test_sarscov2_reference:
	name: Run pipeline test (reference)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Install Nextflow
	run: \|
	wget -qO- get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Run pipeline test (reference)
	run: \|
	nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml

	test_sarscov2_timeseries:
	name: Run pipeline test (test_sarscov2_timeseries)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Install Nextflow
	run: \|
	wget -qO- get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Run pipeline test (timeseries)
	run: \|
	nextflow run main.nf -profile docker --prefix "covidmvp-timeseries-$(date +%Y-%m-%d)" -params-file covidmvp_timeseries_params.yaml

	check_success:
	name: Check if all tests passed
	needs:
	[test_sarscov2_user, test_sarscov2_reference, test_sarscov2_timeseries]
	runs-on: ubuntu-latest
	steps:
	- name: Check job status
	if: ${{ failure() }}
	run: exit 1

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