CWL fixes and dependencies update #10

	# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven

	# This workflow uses actions that are not certified by GitHub.
	# They are provided by a third-party and are governed by
	# separate terms of service, privacy policy, and support
	# documentation.

	name: Maven Build

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	- name: Set up JDK 11
	uses: actions/setup-java@v3
	with:
	java-version: '11'
	distribution: 'temurin'
	cache: maven
	- name: Build, test and package with Maven
	run: mvn -B package --file pom.xml
	- name: Install CWL env
	run: \|
	sudo apt-get -y install python3 python3-pip
	pip3 install cwlref-runner
	- name: Test CWL generation
	run: \|
	git clone https://github.com/Workflomics/domain-annotations
	cd domain-annotations
	java -jar ../target/APE-*-executable.jar ./WombatP_tools/config.json
	cd ./WombatP_tools/CWL
	cwltool --enable-dev --validate workflowSolution_0.cwl

	# Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
	- name: Update dependency graph
	uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6

Provide feedback