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Add cubi-tk snappy zap-output #45

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holtgrewe opened this issue Jun 14, 2021 · 0 comments
Open

Add cubi-tk snappy zap-output #45

holtgrewe opened this issue Jun 14, 2021 · 0 comments
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enhancement New feature or request

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@holtgrewe
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Is your feature request related to a problem? Please describe.
In snappy-pipeline, a common problem with meta data is that assignment to families is (partially) incorrect. E.g., a trio might actually be processed as two disjoin families or samples may be swapped between families.

Describe the solution you'd like
A common resolution is to clear all work and output file that contain the samples in the families. Tools support would be nice.

  • With knowledge about the snappy-pipeline structure, look for all work and output files that have sample names in them (e.g., .ped or .vcf.gz files).
  • Collect a list of such files and ask user to confirm to delete them (add a --yes parameter to answer question(s) with yes).
  • Remove files if user confirmed.

Describe alternatives you've considered
N/A

Additional context
In some cases, it may be necessary to remove "merge" in steps as well.

@holtgrewe holtgrewe added the enhancement New feature or request label Jun 14, 2021
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