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Description
Describe the bug
The Sodar / cubi-tk isa-tab template have been modified not use the Library Name column anymore, since this is not actually ISA compliant.
However, the cubi-tk sodar add-ped function will treat all Extract Name column the same and only write the expected content of the "last material column" into a column named Library Name.
To Reproduce
Steps to reproduce the behavior:
- Create a new DNA germlin (or cancer?) samplesheet with Sodar GUI or cubi-tk
- Use the template in a Sodar project
- Upload new sample data using
cubi-tk sodar add-ped - Both
Extract Namecolumns have the same content
Expected behavior
The 2nd Extract Name Column should be treated the same as Library Name
Additional context
I think recent changes to cubi-tk snappy pull-samplehseet already contain the code that can fix this.
We should also consider re-factoring all the ISA graph parsing code that is used/overwritten by different functions.
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