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_build_ngs_library_to_kit function in sv_calling_targeted step requires GCNV subconfig #594

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Nicolai-vKuegelgen opened this issue Jan 16, 2025 · 0 comments

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@Nicolai-vKuegelgen
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Describe the bug
Currently the _build_ngs_library_to_kit function in sv_calling_targeted references the gcnv subconfig in the init of the workflow step setup (or rather specifically the "path_target_interval_list_mapping" list of that subconfig).
Given that gcnv is only one optional tool usable in ht workflow this is sub-optimal at best.

To Reproduce
Steps to reproduce the behavior:

  1. Do not configure gcnv subconfig for the sv_calling_targeted step
  2. Run sv_calling_targeted
  3. See error

Expected behavior
The workflow should work without the need to define specific subconfig entries.
Additionally it seems like the _build_ngs_library_to_kit function (which derives the matching of samples to a target region bed file, via the library kit entry of the biomedsheet samplesheet) is used in several different places & and workflows but is always defined individually instead of centrally, which woulr probably be a better solution (maybe something like [germline-]library_kit_finder Mixin)

Additional context
The varfish_export also has a _build_ngs_library_to_kit function, which uses the (equivalently defined/build) "path_target_interval_list_mapping" entry of the (parent) ngs_mapping workflow.

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