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Organize each variant caller into its own subworkflow #9

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Tracked by #17
rnaidu opened this issue Sep 12, 2024 · 1 comment
Closed
Tracked by #17

Organize each variant caller into its own subworkflow #9

rnaidu opened this issue Sep 12, 2024 · 1 comment
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enhancement New feature or request

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@rnaidu
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rnaidu commented Sep 12, 2024

Description of feature

Re-organizing nucleovar.nf to make sure each Variant Caller (VarDict,MuTect,MuTect2) is called in a separate subworkflow. This is in order to compartmentalize the code and keep nucleovar.nf concise.

Steps in each variant caller subworkflow:

  • Variant Caller module
  • Variant Caller Filtering
  • BCFTools Suite (gzip,norm,sort,concat)

Final output of each subworkflow is a concatenated VCF file that will be annotated against each variant caller.

@rnaidu rnaidu added the enhancement New feature or request label Sep 12, 2024
@rnaidu rnaidu self-assigned this Sep 12, 2024
@rnaidu rnaidu mentioned this issue Oct 8, 2024
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@rnaidu rnaidu closed this as completed Oct 10, 2024
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rnaidu commented Oct 10, 2024

included in most recent PR: #17 (comment)

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