readPATH = params.reads
genome = file(params.genome)
iterations = params.itr
outDir = params.out
single = "no"
runDir = params.runDir

genome_base = "${genome.getBaseName()}"
genome_file = "${genome.getName()}"
genome_path = "${genome.getParent()}"

fastqFILES = Channel.empty()

if (readPATH) {
  readFiles = file(readPATH)
  fastqFILES = extractFastq(readFiles)
}

(fastqFILES, readMapping) = fastqFILES.into(2)

process index {
    tag { "Genome: $genome_base" }
    publishDir '$outDir', mode:'copy', overwrite: true
    input:
    file fasta from genome
    output:
    file "${outDir}" into index
    shell:
    """
    Refindex.py --itr 1 --ref ${fasta} --out ${outDir}
    """
    }
process mapping {
    tag { "Mapping: $idSample" }
    publishDir "$outDir", mode:'copy', overwrite: true
    input:
    set idSample, file(read1), file(read2) from readMapping
    file genome_index from index
    output:
    file "${outDir}" into mapping
    script:
    """
    ReadMapping.py --itr 1 --r1 ${fastqFile1} --r2 ${fastqFile2} --out ${outDir}
    """
  }
process assembly {
    tag { "Assembly: $idSample" }
    publishDir "$outDir", mode:'copy', overwrite: true
    input:
    file reads from mapping
    output:
    file "${outDir}" into assembly
    script:
    """
    ContigAssembly.py --itr 1 --out ${outDir}
    """

def extractFastq(readFiles) {
  return fastqFILES = Channel
    .from(readFiles.readLines())
    .map{line ->
      list       = checkTSV(line.split(),4)
      idSample   = list[0]
      idRun      = list[1]
      fastqFile1 = list[2]
      fastqFile2 = list[3]
      //checkFileExtension(FastqFile1,".fastq.gz")
      //checkFileExtension(FastqFile2,".fastq.gz")
      [idSample, idRun, fastqFile1, fastqFile2]
    }
}

def checkTSV(it, number) {
  // Check if TSV has the correct number of items in row
  if (it.size() != number) {
    exit 1, "Malformed row in TSV file: $it, see --help for more information"
  }
  return it
}