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Change behaviour of varfish_export with path_exon_bed #389

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holtgrewe opened this issue Apr 19, 2023 · 0 comments · Fixed by #390
Closed

Change behaviour of varfish_export with path_exon_bed #389

holtgrewe opened this issue Apr 19, 2023 · 0 comments · Fixed by #390

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@holtgrewe
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Is your feature request related to a problem? Please describe.
The varfish_export step currently relies on the the library type on using the BED file for filtering the variants to exons etc.

Describe the solution you'd like
Remove the is_wgs check in the code and only rely on the path_exon_bed setting.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe changed the title Change behaviour Change behaviour of varfish_export with path_exon_bed Apr 19, 2023
holtgrewe added a commit that referenced this issue Apr 20, 2023
@holtgrewe
feat: path_exon_bed can be provided independent of data type (#389)
c12c26c 
Previously, the BED file value was always used for WGS data and never
used for WES data.  Now, it is used when it has been provided (not
the empty string and not null/None).
@holtgrewe holtgrewe linked a pull request Apr 20, 2023 that will close this issue
feat: path_exon_bed can be provided independent of data type (#389) #390
Merged
Nicolai-vKuegelgen pushed a commit that referenced this issue Apr 20, 2023
@holtgrewe
feat: path_exon_bed can be provided independent of data type (#389) (#…
7759d4d 
…390)
@tedil tedil mentioned this issue Jun 28, 2024
Merged
This was referenced Dec 9, 2024
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feat: path_exon_bed can be provided independent of data type (#389) bihealth/snappy-pipeline
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@holtgrewe