github.com/CDPHE/CDPHEnextclade

Automatic Tools and Workflows
1

CDPHEnextclade

WDL for running Nextclade on GCP Terra.

Terra data table should contain 2 columns

  1. entity:sample_id containing the prefix that you would like for your output files (e.g. entity:sample000_id)
  2. multifasta: location (google bucket path) to input your multifasta run Nextclade.

On Terra, inputs should be specified as:

  1. multifasta = this.multifasta
  2. sample_id = this.sample_id (e.g. this.sample000_id depending on how you named your data table)
  3. out_dir = the google bucket
This is a companion discussion topic for the original entry at github.com/CDPHE/CDPHEnextclade