added organism criteria field for final report if species id is null #525

	name: Pipeline 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
	# Only run on push if this is the phac-nml dev branch (merged PRs)
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'phac-nml/mikrokondo') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.04.0"
	- "latest-everything"
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

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

	- name: Cache nf-test installation
	id: cache-software
	uses: actions/cache@v3
	with:
	path: \|
	/usr/local/bin/nf-test
	/home/runner/.nf-test/nf-test.jar
	key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest

	- name: Install nf-test
	if: steps.cache-software.outputs.cache-hit != 'true'
	run: \|
	wget -qO- https://code.askimed.com/install/nf-test \| bash
	sudo mv nf-test /usr/local/bin/

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

	- name: Run nf-test
	run: \|
	nf-test test

	- name: Nextflow run with test profile
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

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