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Clinical-Genomics-Lund / SomaticPanelPipeline

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coyote cli preparations #61

Closed ViktorHy closed 3 months ago

ViktorHy commented 3 months ago

Added two new functions:

CNVs as JSON

Added a parallel track to CNVs to generate JSON output compatible with coyote_cli. This included a new module for bedtools which should be configurable with external arguments in configs. As of now it does not merge the normal and tumor outputs

COYOTE_YAML

Added a parallel track to generate yaml-output for coyote_cli. Basically a copy of the old COYOTE module but data output as yaml file to be loaded with coyote_cli yaml function

ViktorHy commented 3 months ago

just realized I never send the cnv json over to the new coyote_yaml function

ramsainanduri commented 3 months ago

just realized I never send the cnv json over to the new coyote_yaml function

I think you are still working on it

ViktorHy commented 3 months ago

yeah, and I got really stuck as well. Think I have a commit coming in today

ViktorHy commented 3 months ago

@ramsainanduri ok now I got a working workflow for JSONs