github.com/CDPHE/classifyCOVIDlineage

Automatic Tools and Workflows
1

classifyCOVIDlineage

Takes the consensus fasta SARS-CoV-2 genome assembly outputs of IlluminaPreprocessAssembly.wdl and NanoporeGuppyAssembly.wdl and:

  1. uses Pangolin to assign PangoLineages
  2. uses Nextclade to assign clade
  3. exports the outputs to your chosen google bucket

The google bucket to which the outpus should be sent should be set as a Terra input as a String in double quotes

This is a companion discussion topic for the original entry at github.com/CDPHE/classifyCOVIDlineage