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Is there a good way to test CWL tools and workflows?

I'm getting started writing CWL tools and workflows. I would like to get a good testing framework setup from the beginning. Is there something that can help testing CWL? How are you testing CWL?

I saw cwltest exists. However, the documentation is very sparse. I haven't figured out what should go inside test-descriptions.yml. It is also not clear to me if this tool is just checking for syntax errors, or will it actually try to run a tool or a complete workflow.

Thanks, Carlos

cwl
• 4,933 views • link
updated by Martín • Martín • written by Carlos Borroto Carlos Borroto

I don't have a full answer here, but some suggestions would be:

  1. Testing with cwltool and the --js-console and --debug options. Also using --tmp-outdir-prefix, -leave-tmpdir, and --leave-outputs to inspect results from intermediate steps

  2. Having small sample inputs that can be used to run the workflows quickly when making changes

  3. Testing the individual tools before the whole workflows

  4. cwltool --validate to only validate the workflow and not run it

  5. cwltool --print-dot and cwltool --print-rdf to show graph of the workflow

• 0 views • link
written by ionox0 ionox0

cwltest is for the execution of CWL tools and workflows and comparing their outputs with an expected result or an expected failure.

ionox0 comment should be changed to be an answer, as that is basically my response.

• 1 views • link
written by Michael R. Crusoe Michael R. Crusoe

2 answers

https://www.commonwl.org/#Editors_and_viewers lists tools to assist with CWL composition, including a graphical user interface and plugins for many popular IDEs (Atom, vim, emacs, Visual Studio Code, IntelliJ, gedit). Some of these plugins will do a basic syntax check for you as well.

• 2 views • link
written by Michael R. Crusoe Michael R. Crusoe

Added as answer per @mr-c comment

Some suggestions would be:

  1. Testing with cwltool and the --js-console and --debug options. Also using --tmp-outdir-prefix, -leave-tmpdir, and --leave-outputs to inspect results from intermediate steps

  2. Having small sample inputs that can be used to run the workflows quickly when making changes

  3. Testing the individual tools before the whole workflows

  4. cwltool --validate to only validate the workflow and not run it

  5. cwltool --print-dot and cwltool --print-rdf to show graph of the workflow

• 1 views • link
written by ionox0 ionox0

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