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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:
bwa_mem2 has largely replaced bwa
gatk4_hc_gcvf has largely replaced gatk_hc
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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: