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Reduce verbosity of cromwell run

Redmar_van_den_BergRedmar_van_den_Berg Member ✭✭

Is there a way to reduce the verbosity of cromwell run? It prints a lot of information, in very long lines, which makes it difficult to see where exactly things went wrong if a workflow fails. I noticed that the logs in cromwell-workflow-logs are a lot cleaner, and tend to only print out the more relevant information, like [UUID(f01048ab)]: Starting calls: variantDiscovery.genotype:6:1, or java.lang.Exception when something goes wrong.

Is there a way to disable the additional output that cromwell run generates? I had a look at the settings file for cromwell but nothing seemed relevant to this issue.

Edit: It looks like this got placed in the gatk forum by mistake, feel free to move it to the wdl forum.

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @Redmar_van_den_Berg, I've moved this question to the WDL forum. The team should get to your question shortly.

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