main.nf

nextflow.enable.dsl=2

include {qc} from "./workflows/quality_control.nf"
include {pangenome} from "./workflows/pangenome.nf"
include {localisation} from "./workflows/localisation.nf"


workflow {
  fasta_dataset = Channel
    .fromPath(params.input)
    .ifEmpty{exit 1, "Fasta files not found not found: ${params.input}"}
  
  def valid_params = [
    pangenome: ['roary', 'panaroo', 'pirate'],
    gram: ['pos', 'neg'],
    localisation: ['psortb']
    ]
    
  //could loop this but probably better to have a clear and concise message?
  if(!valid_params["pangenome"].contains(params.pangenome)){
    exit 1, 'Invalid pangenome tool, must be roary, panaroo or pirate' 
    }
      
  if(!valid_params["gram"].contains(params.gram)){
    exit 1, 'Invalid Gram stain parameter for Prokka, must be pos or neg'
    }

  if(!valid_params["localisation"].contains(params.localisation)){
    exit 1, 'Invalid localisation tool, must be psortb'
    }

  main:
    qc(fasta_dataset)
    pangenome(fasta_dataset)
    localisation(pangenome.out.pan_genome_reference)

}