[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] `fastq-scan` updates & improvements. Adding JSON as wf output file #1821

	#
	# This workflow will run on Pushes and Pull Requests against the main branch. It
	# will only run "miniwdl check" on wdl files that have had a change in the push
	# or PR.
	#
	name: MiniWDL Check
	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]

	jobs:
	changes:
	name: Check for changes
	runs-on: ubuntu-latest
	outputs:
	# Expose workflows with changes
	workflows: ${{ steps.filter.outputs.wf }}
	workflows_files: ${{ steps.filter.outputs.wf_files }}
	steps:
	# Checkout the repo
	- uses: actions/checkout@v4

	# Select wdl files with changes
	- uses: dorny/paths-filter@v3
	id: filter
	with:
	filters: \|
	wf:
	- added\|modified: 'tasks/**'
	- added\|modified: 'workflows/**'
	list-files: json

	check:
	runs-on: ubuntu-20.04
	name: ${{ matrix.wf }}
	needs: changes
	if: ${{ needs.changes.outputs.workflows != '' && toJson(fromJson(needs.changes.outputs.workflows)) != '[]' }}
	strategy:
	fail-fast: false
	matrix:
	wf: ${{ fromJson(needs.changes.outputs.workflows_files) }}
	steps:
	# Checkout the repo
	- uses: actions/checkout@v4

	# Install a version of Python3
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.x"

	# Install MiniWDL (WDL syntax) and ShellCheck (shell syntax)
	- name: install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get -y install shellcheck
	pip3 -q install miniwdl 'importlib-metadata==4.13.0'

	# Run MiniWDL check on each of the changed WDLs
	- name: MiniWDL Check ${{ matrix.wf }}
	run: miniwdl check ${{ matrix.wf }}

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