8000 DSL2 - Genotyping on unmerged libraries · Issue #1128 · nf-core/eager · GitHub
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DSL2 - Genotyping on unmerged libraries #1128

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ilight1542 opened this issue Mar 26, 2025 · 1 comment
Open

DSL2 - Genotyping on unmerged libraries #1128

ilight1542 opened this issue Mar 26, 2025 · 1 comment
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DSL2 enhancement New feature or request

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@ilight1542
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Aida mentioned that the default behavior of always collapsing libraries within a single sample for input into genotyping may be inappropriate when mutliple libs have different UDG treatment status/damage models, etc.

Modifying necessary for the input channel generation for genotyping to be able to either get unmerged or merged data.

Unmerged data also necessitates changes to the prefix and tags for all processess where previously only unique sampleIDs would be sufficient.
@ilight1542 ilight1542 added enhancement New feature or request DSL2 labels Mar 26, 2025
@ilight1542 ilight1542 self-assigned this Mar 26, 2025
@ilight1542 ilight1542 mentioned this issue Mar 26, 2025
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@TCLamnidis
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@aidaanva @ilight1542
Was looking through the PR for the second time, when I realised I am not entirely sold on the idea. Sorry if this is not the first time you have to explain it (it could be my lack of coffee atm), but I did not see this discussion documented anywhere:

  • Is this added complexity actually needed?
  • How would this be different from the user tweaking their TSV file to give each library a different Sample_ID? Unless the genotypes from each library get merged to a sample level eventually? But aren't we then back to square one?

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