[Feature]: Allow passing arbitrary genome list

[MillironX]

Summary

Create a new parameter that allows for passing a user-created list of genomes to compare the virus sequences against, in addition to the pre-defined lists.

Added Features

Additional Modified parameters

• --genome_list
  • type: String
  • default: jev
  • Path to TSV file containing NCBI accession numbers of strains for constructing phylogenetic trees. Preset genome lists can be specified by name

More Info

Context

Right now, only Japanese Encephalitis Virus has a list of genomes to compare against as a preset for the pipeline, and which genomes were included was @MillironX's judgement call. There should be an option to pass an arbitrary genome list to the pipeline. If we want to sequence anything else, or pick a different group of genomes to compare against,

Possible implementation

1. Check to see of params.genome_list is a valid path
   1. Create a file object with value params.genome_list
2. Check if params.genome_list is included in the Genomes directory
   1. Create a file object with value "${workflow.projectDir}/genomes/${params.genome_list}"
3. Check if "${params.genome_list}.tsv" is included in the Genomes directory
   1. Create a file object with value "${workflow.projectDir}/genomes/${params.genome_list}.tsv"
   2. No matches: throw error