bihealth / cubi-isa-templates

CUBI ISA-Tab templates

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Add new isatab template 'cancer'

sellth opened this issue · comments

Discussed this with @mbenary. Current templates tumor_normal_dna & *_triplets are unsatisfactory in multiple ways, not the least by relying on external config injection for "triplets":

configuration=load_variables("isatab-tumor_normal_triplets", {"is_triplet": True}),

We therefore decided to start a better named and hopefully more useful singular cancer template.

To do

  • copy tumor_normal_triplets files as a basis
  • adapt is_triplet logic to selectively add transcriptomics assay within the template
  • add human readable prompts
  • get feedback from @mbenary & @ericblanc20,
  • discuss addtional changes (i. e. removing not used protocol parameters)
  • remove tumor_normal_* templates?