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Alphanumerical ID naming system in Cromwell


I have been using Cromwell/WDL for sometime now and I am still trying to figure out some of the nuances associated with it. I am currently trying to formulate a MultiSample MultiStep Variant Calling Workflow and I am actually having trouble with the naming system thats being used for the successful runs. For eg if I am running a workflow that is operating on 25 samples at a time, at the end of the workflow there is random ID that is generated and there is also a directory created with the same name. Inside that directory there is a separate folder for each of the sample.

May I know if I can give these folders a meaning full name by defining the name somewhere in my wdl code or do I have to do it Manually after every run. The reason I ask is, if I wanna go back and check a certain output it becomes tough to check each folder to see if thats the one with the information that I require.

I would also like to take this opportunity to thank the wdl team for your prompt responses for the queries I have posted in the past.


Best Answer


  • mcovarrmcovarr Cambridge, MAMember, Broadie, Dev

    Hello @ramshankar1990, this alphanumerical ID is the workflow ID Cromwell assigns when it accepts a workflow submission. When a workflow is submitted Cromwell returns the assigned workflow ID in the submission response. So if you capture these workflow IDs you should know which UUID corresponds to which submission.

  • Hello, thank you very much, this is good to know. I will pursue it.

    Could you please also help me with the second part of my question? I would like the output folder for each sample to be named according to the sample name, e.g. NA12878/, as opposed to shard1/

    Is there a way to do this dynamically from within my workflow code? I could probably have my code rename output folders after the workflow has finished running, but that would not help my analysts debug the workflow if there is a failure mid-run. Any suggestion would be appreciated.

    Thanks much!

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