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I would like to run the CNVkit workflow on Cancer Genomics Cloud.

However, the two workflows that I'd like to use:

don't have parameters that can be set to define in which folder to save the results or which prefix to add to the results. This means that if you're generating multiple references or calling CNV for multiple tumor samples you will end up with results having the same name for each run (tumor).

I tried to modify the CWL workflow, online and through Rabix composer, but I was unable to make it work. I would like to use the published workflow to not code everything from the ground up.

Do you know how to update/use the current CWL workflow in order to avoid having the same filename/folder for all the results?

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    $\begingroup$ @llrs updated question with links to the workflows' code $\endgroup$
    – gc5
    Feb 6 '19 at 15:50
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If the output is File, you can add this step https://github.com/Barski-lab/workflows/blob/master/tools/rename.cwl to rename the output file.

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