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Update defaults for snappy itransfer-* tools #191

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Nicolai-vKuegelgen opened this issue Sep 7, 2023 · 1 comment
Open

Update defaults for snappy itransfer-* tools #191

Nicolai-vKuegelgen opened this issue Sep 7, 2023 · 1 comment

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@Nicolai-vKuegelgen
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Nicolai-vKuegelgen commented Sep 7, 2023

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.

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

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