Nf test local subworkflows #3

	name: nf-test coverage
	# 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]
	workflow_dispatch:

	env:
	NXF_ANSI_LOG: false

	jobs:
	coverage:
	name: Determine test coverage
	# Only run on push if this is the nf-core dev branch (merged PRs)
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'nf-cmgg/germline') }}"
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
	with:
	fetch-depth: 0

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v2

	- name: Install nf-test
	run: \|
	conda install -c bioconda nf-test

	- name: Determine coverage
	id: coverage
	run: \|
	output=$($CONDA/bin/nf-test coverage --silent \| grep -vE "^(Load\|Warning\|Files)")
	echo $output
	files=$(echo $output \| grep " •")
	coverage=$(echo $output \| grep "COVERAGE")
	echo "::set-output name=files_output::$files"
	echo "::set-output name=coverage_output::$coverage"

	- name: Comment coverage
	uses: bubkoo/auto-comment@v1
	with:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	pullRequestOpened: >
	nf-test coverage 🚀

	${{ steps.coverage.outputs.coverage_output }}

	<details>

	<summary>File view</summary>

	${{ steps.coverage.outputs.files_output }}

	</details>

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