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Describe the bug
By default the 'pedigree_field' value in the config setting for any given dataset in not defined or empty. This means that snappy will not combine family members from any family that are not connected by a parent. This behavior would usually be intended and therefore a default for the 'pedigree_field' should be set ("familyId" is the corresponding biomedsheets column currently used in most projects).
To Reproduce
Steps to reproduce the behavior:
Setup a snappy project (i.e. with cubi-tk) that has a familyId definitions
Use the default or an older config file that is missing the pedigree_field entry
Snappy will run but not combine family members as expected
Expected behavior
The "familyId" should be default pedigree_field value. Potentially with a fallback to the current default behaviour if this column is not present in any given samplesheet.
The text was updated successfully, but these errors were encountered:
Describe the bug
By default the 'pedigree_field' value in the config setting for any given dataset in not defined or empty. This means that snappy will not combine family members from any family that are not connected by a parent. This behavior would usually be intended and therefore a default for the 'pedigree_field' should be set ("familyId" is the corresponding biomedsheets column currently used in most projects).
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The "familyId" should be default pedigree_field value. Potentially with a fallback to the current default behaviour if this column is not present in any given samplesheet.
The text was updated successfully, but these errors were encountered: