nf_download_Genomes

#!/usr/bin/env nextflow

// Last modified 13 October 2020

// Enable modules
nextflow.enable.dsl=2

params.input = ''
params.outdir = './'

params.assembly = 'FALSE'
params.annotation = 'TRUE'


params.verbose = false

params.help = false
// Show help message and exit
if (params.help){
    helpMessage()
    exit 0
}

include { DOWNLOAD_GENOMES }          from './nf_modules/genomes.mod.nf'


workflow {

    main:
    input_genomes = Channel
                        .fromPath( params.input )
                        .splitCsv()
                        .map{ row -> [ row[0], row[1] ]} // here the file can have many columns but we filter them

    DOWNLOAD_GENOMES    (input_genomes, params.outdir, params.assembly, params.annotation)
}