Differences in Pangolin2 task inputs

[jvhagey]

Current code for task_taxonID.wdl pangolin2 task lines 119-121 looks like this:

pangolin "~{fasta}" \
--outfile "~{samplename}.pangolin_report.csv" \      
--verbose

The code for Theiagen's fork of the same task lines 111-115 looks like this:

task pangolin2 {  
input {    
File        fasta    
String    samplename    
Int         min_length=10000   
Float     max_ambig=0.5    
String    docker  
}
  command 
  <<<   
  # date and version control    
  date | tee DATE    set -e

    pangolin "~{fasta}" \      
     --outfile "~{samplename}.pangolin_report.csv" \       
     --min-length ~{min_length} \       
     --max-ambig ~{max_ambig} \      
     --verbose

We might need to consider adding --min-length and --max-ambig parameters to toolkit version to avoid differences in pangolin calls between Terra and CLI versions.