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Create a Subworkflow for Variant calling #84

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8 of 9 tasks
jimmyliu1326 opened this issue Nov 20, 2024 · 1 comment
Open
8 of 9 tasks

Create a Subworkflow for Variant calling #84

jimmyliu1326 opened this issue Nov 20, 2024 · 1 comment
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@azmigueldario @mayee123
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enhancement New feature or request

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@jimmyliu1326
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jimmyliu1326 commented Nov 20, 2024 •
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Description of feature

Create a sub-workflow for variant calling and variant filter.

The following modules require writing nextflow modules before integration:

  • Snippy
  • Snippy_core
  • medaka_variant
  • Gubbins
  • core-snp-filter
  • Nucmer
  • delta2vcf
  • Write subworkflow
  • Solve integration with rest of pipeline
@jimmyliu1326 jimmyliu1326 added the enhancement New feature or request label Nov 20, 2024
@azmigueldario
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azmigueldario commented Nov 27, 2024 •
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Testing of core-snp-filter and gubbins is missing
Also check integration of preliminary steps with snippy
Still have to write subworkflow, only drafted

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@azmigueldario azmigueldario

@mayee123 mayee123

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@jimmyliu1326 @azmigueldario @mayee123