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bihealth / cubi-tk

CUBI Tooling for SODAR, VarFish et al.
MIT License
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Update defaults for snappy itransfer-* tools #191

Open Nicolai-vKuegelgen opened 1 year ago

Nicolai-vKuegelgen commented 1 year ago

Is your feature request related to a problem? Please describe. The cubi-tk snappy itransfer-* modules allow streamlined upload of snappy results to Sodar. However, the currently defined default tools do not match the most commonly used tools (in medGen projects) anymore:

Describe the solution you'd like The defaults in cubi-tk should match to most commonly used tools.

Altrernative Solution In case multiple tools are commonly in use, it would be nice if cubi-tk coul either read the snappy_pipeline/config.yaml file to find one or all used tools in a given project or if the ~/.cubitkrc.toml file could be used to set user specific defaults.

Nicolai-vKuegelgen commented 1 year ago

@ericblanc20 Do you also use these tools for the somatic projects? What are your most commonly used mapper / variant caller tools there?