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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Bug: cg workflow raredisease panel error #3770

Closed peterpru closed 3 weeks ago

peterpru commented 3 weeks ago

Describe the bug When doing cg workflow raredisease panel the command exits with an error regarding the genome build. When genome is not set, it exits with error 'NoneType', when the genome build is given for a sample, it will exit as shown in the screenshot with a cg.exc.CgError: Reference GRCh37 has no associated genome build for panels: GRCh37.

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To Reproduce Steps to reproduce the behavior:

  1. Run cg workflow raredisease panel <CASE> in us

Expected behavior A gene panel file should be generated.

Additional context Add any other context about the problem here.

peterpru commented 3 weeks ago

Problem solved: cg expects the reference genome build to be hg19 for build 37.

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When setting reference genome to be hg19 for the samples in the case, the command succeeds: image

peterpru commented 3 weeks ago

When running the cg workflow raredisease panel command directly, hg19 is converted to 37 by cg when talking to Scout, and the command completes successfully. When doing cg workflow raredisease start, the command fails as hg19 is translated to be hg19 for the managed variants command, and not one of the allowed options: image

peterpru commented 3 weeks ago

The scout export command used for managed variants defaults to 37 if no reference genome is given, which is why it worked before. image

peterpru commented 3 weeks ago

Fixed in https://github.com/Clinical-Genomics/cg/pull/3772, where hg19 as input is converted to 37 for the managed variants-buildinput.