How do I get intermediate outputs from cromwell

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Matthias De Smet

• December 15, 2020 09:59

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: NA
b) Exact command used:  NA
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Hi,

I'm developing a workflow, which strings together a bunch of subworkflows. I'd like to get "intermediate" outputs from those subworkflows, while the bigger flow is still running. Is there a way to achieve this?

e.g. workflow consists of demultiplexing, then mapping, then qc. I'd like to get the demultiplexing results while the data is still mapping.

 

Thanks

M

 

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  Genevieve Brandt (she/her)

  • January 05, 2021 22:40

  Hi Matthias De Smet,

  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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