Question: Is there a way to use your tool to convert WDL to CWL format

[michael-kotliar]

Not an actual issue, just a question. Is there any way to use your tool to convert WDL into CWL format? Or, at least, parse WDL into some objects that are compatible with source code from cwltool?

Thanks!

[illusional]

Hey @michael-kotliar! I've been working on a WDL parser in #69, it's not wrapped up nicely yet in the tool suite, but you could use it to convert some workflows. Note the limitations in the description of #69.

Here's a direct link to the script: https://raw.githubusercontent.com/PMCC-BioinformaticsCore/janis-core/master/janis_core/ingestion/fromwdl.py
You'll have to have janis-core + MiniWDL installed, you could change the last line (L447) to translate"cwl" instead of "janis", and then run the script directly:

python3 fromwdl.py <yourscript.wdl>

[michael-kotliar]

Hi @illusional,
Great! Thanks for the script!

[illusional]

How'd you go @michael-kotliar?

[michael-kotliar]

It works fine. I tested it with a simple WDL workflow that I had and I was able to run it with cwltool. I think I had to make some changes in the code to generate outputs, but for now, I anyway use it only for testing purposes. However, I hope that this script will evolve and will cover more features from WDL:)