Update fq.wdl #501

	name: pytest-workflow Check

	on: [push]

	jobs:
	list-tags:
	runs-on: ubuntu-latest
	outputs:
	tags: ${{ steps.set-tags.outputs.tags }}
	steps:
	- name: checkout
	uses: actions/checkout@v4
	- name: set tags
	id: set-tags
	run: echo "tags=$(find tests -name '*.yaml' -exec yq --output-format yaml '.[].tags[] ' {} \;\| sort \| uniq \| grep -vE 'deprecated\|miniwdl\|cellranger' \| jq -ncR '[inputs]')" >> $GITHUB_OUTPUT
	pytest_check:
	needs: list-tags
	runs-on: ubuntu-latest
	strategy:
	matrix:
	tag: ${{ fromJson(needs.list-tags.outputs.tags) }}
	steps:
	- uses: actions/checkout@v4
	with:
	lfs: true
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'
	- name: Install miniwdl and pytest-workflow
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements-dev.txt
	- name: filter tests
	run: \|
	find tests -name '*.yaml' -exec yq --output-format yaml -i 'del(.[] \| select(.tags[] \| test("reference\|deprecated\|cellranger") ) )' {} \;
	- name: Run pytest-workflow
	run: \|
	pytest --git-aware --basetemp /home/runner/work/pytest --symlink --tag ${{ matrix.tag }}

Provide feedback