You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Describe the bug
Sometimes sex information in the (biomedsheet) samplesheet needs to be updated or newly sequenced members are added to a family. This update should also lead to according changes in ped files and and all other relevant files.
To Reproduce
Steps to reproduce the behavior:
Run snappy with sex information (i.e. unknown sex that crashes gcnv)
Update the sex information in the samplesheet
Restart any snappy step that includes the WritePedigreeStepPart (i.e. sv_calling_targeted)
write_pedigree is not rerun
Expected behavior
A change in the input (meta)data should trigger a rerun of all affected downstream files.
Additional context
The current input for write_pedigree seems to only include bam files.
The rerun triggers for number/set of input files should be re-enabled to catch addition of family members
A rerun trigger on params could be used to forward sex changes to snakemake
The text was updated successfully, but these errors were encountered:
Nicolai-vKuegelgen
changed the title
Rerun of write_pedigree step is not triggerd when sex infiormation in samplesheet is updated
Rerun of write_pedigree step is not triggerd when sex information in samplesheet is updated
Oct 13, 2023
Additon: it seems like this extends to other changes of the ped/family structure as well. I.e. addition a new family member will not trigger a re-write of the ped file to include this update.
Nicolai-vKuegelgen
changed the title
Rerun of write_pedigree step is not triggerd when sex information in samplesheet is updated
Snakemake rerun triggers do not check for changes in ped structure and content
Nov 22, 2023
Describe the bug
Sometimes sex information in the (biomedsheet) samplesheet needs to be updated or newly sequenced members are added to a family. This update should also lead to according changes in ped files and and all other relevant files.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
A change in the input (meta)data should trigger a rerun of all affected downstream files.
Additional context
The text was updated successfully, but these errors were encountered: