Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

The dataset config pedigree_field should not be empty by default #471

Open
Nicolai-vKuegelgen opened this issue Nov 22, 2023 · 0 comments
Open

Comments

@Nicolai-vKuegelgen
Copy link
Contributor

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:

  1. Setup a snappy project (i.e. with cubi-tk) that has a familyId definitions
  2. Use the default or an older config file that is missing the pedigree_field entry
  3. 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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant