How do I keep a glob from copying a file in Cromwell / WDL

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Gregory Dougherty

• March 09, 2021 00:24

Using Crowell 52.  When I do a glob to get matching files, Cromwell places a copy of each matching file in the glob-* directory.

 

As these are multi-gigabyte Bam files, I'd really prefer for Cromwell to store soft links to the files, rather than full copies.

 

Is it possible to make this happen?

 

Thank you.

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  Genevieve Brandt (she/her)

  • March 10, 2021 18:11

  Hi Gregory Dougherty, our GATK support team is focused on questions involving GATK issues or abnormal results. You can see our support policy here. For questions regarding Cromwell, we encourage other users to help each other find solutions. You can also look at these resources for more information:

  • Bioinformatics Stack Exchange
  • Cromwell slack organization: cromwellhq.slack.com
  • Cromwell Documentation
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