21 wildcard input handling #84

	name: Cromwell Test Run

	on:
	pull_request:
	workflow_dispatch:

	jobs:
	generate-matrix:
	runs-on: ubuntu-latest
	outputs:
	matrix: ${{ steps.set-matrix.outputs.matrix }}
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Find WDL Directories
	id: set-matrix
	run: \|
	# Find all directories containing .wdl files
	dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; \| sort -u \| sed 's\|^\./\|\|' \| jq -R . \| jq -s \| jq -c .)
	echo "Directories: $dirs"
	echo "matrix=$dirs" >> $GITHUB_OUTPUT

	testrun:
	needs: generate-matrix
	if: ${{ github.event.pull_request.head.repo.fork == false }}
	runs-on: ubuntu-latest
	permissions: write-all
	strategy:
	matrix:
	wdl: ${{ fromJson(needs.generate-matrix.outputs.matrix) }}
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Set Up Java
	uses: actions/setup-java@v4
	with:
	distribution: 'temurin'
	java-version: '21'

	- name: Pull Cromwell Jarfile
	run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/cromwell-86.jar

	- name: Install uv
	uses: astral-sh/setup-uv@v5
	with:
	version: "0.5.16"

	- name: Set up Python
	run: uv python install 3.13

	- name: Install dependencies
	run: uv sync --all-extras

	- name: Execute Test Run of WDL Workflows
	env:
	CROMWELL_PATH: cromwell-86.jar
	run: uv run pytest tests/cromwelljava/test-run.py --wdl-path=${{ matrix.wdl }} --verbose -s

Provide feedback