Setting a minimum variant cutoff for Freyja

[DrB-S]

Is there a way to set a minimum variant cutoff to 1%? I take it that means setting the abundance to 0.01 in Freyja. Would that be using the Freyja eps option (--eps 0.01)? And if so, is there a config I can edit to set that, or can it be set on the command-line when running Cecret?

[erinyoung]

For Freyja demix? Yes, there are currently two ways to do this:

1. using the freyja_demix_options parameter A. On the command line: --freyja_demix_options "--eps 0.01", but this has a "--" which may cause issues with some versions of nextflow) B. In a config file:

   params.freyja_demix_options = "--eps 0.01"

   2. Setting the task.ext.arg in a "process" scope in a config file

      process {
      withName:freyja_demix {
       ext.args = "--eps 0.01"
      }
      }

When I tested these parameters, this generally causes the workflow to take longer and reduces the number of lineages that freyja identifies.

[DrB-S]

Thanks! It worked with the "--" on the command-line.