Adding array operations unit test WDL #21

	name: WOMtool Validation of WDL Script

	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

	womtoolval:
	needs: generate-matrix
	if: ${{ github.event.pull_request.head.repo.fork == false }}
	runs-on: ubuntu-latest
	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 WOMtool Jarfile
	run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/womtool-86.jar

	-
	name: Validate WDL Scripts
	run: \|
	cmd="java -jar womtool-86.jar validate ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl"
	if [[ -f "${{ matrix.wdl }}/inputs.json" ]]; then
	cmd="$cmd -i ${{ matrix.wdl }}/inputs.json"
	fi
	echo "Running command: $cmd"
	eval "$cmd"

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