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cubi-tk sodar add-ped expects the Library Name Column to exist #267

@Nicolai-vKuegelgen

Description

@Nicolai-vKuegelgen

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:

  1. Create a new DNA germlin (or cancer?) samplesheet with Sodar GUI or cubi-tk
  2. Use the template in a Sodar project
  3. Upload new sample data using cubi-tk sodar add-ped
  4. Both Extract Name columns 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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