kpi_local.nf

#!/usr/bin/env nextflow

/*
 * Given 25mer hit counts, interpret KIR genotypes and
 * haplotypes.
 *
 * Input files end with kmcNameSuffix (default '_hit.txt') and are
 * located in kmcDir.
 *
 * Output files end with '_prediction.txt' in resultDir.
 *
 * @author Dave Roe
 * @todo remove the '_hits.txt' files.
 */

nfForks = 8 // run this many input text files in parallel
// input: kmc probe txt files
kmcNameSuffix = '_hits.txt'          // extension on the file name
params.input = '/Users/daver/gonl/results_v7/hits_test/'
bin1Suffix = 'bin1'
params.output = '/Users/daver/gonl/results_v7/predictions_test/'
probeFile = '/Users/daver/git/kpi/input/markers.fasta'
haps = '/Users/daver/git/kpi/input/haps.txt'
params.allOut = "0"

// things that probably won't change per run
kmcDir = params.input
resultDir = params.output
allOut = params.allOut
if(!kmcDir.trim().endsWith("/")) {
	kmcDir += "/"
}
if(!resultDir.trim().endsWith("/")) {
	resultDir += "/"
}
kmcPath = kmcDir + '*' + kmcNameSuffix
kmcs1 = Channel.fromPath(kmcPath).ifEmpty { error "cannot find any ${kmcNameSuffix} files in ${kmcPath}" }.map { path -> tuple(sample(path), path) }
kmcs2 = Channel.fromPath(kmcPath).ifEmpty { error "cannot find any ${kmcNameSuffix} files in ${kmcPath}" }.map { path -> tuple(sample(path), path) }

/*
 * kmc2locusBin
 *
 * Given a kmc output file, bin the hit reads into separate files based on locus.
 * 
 * e.g., ./kmc2Locus2.groovy -j 100a.txt -p kmers.txt -e bin1 -o output
 * 
 * Input files: e.g., 100a.fasta
 * Output files have an extension of 'bin1'.
 */
process kmc2locusBin {
//  publishDir resultDir, mode: 'copy', overwrite: true
//  maxForks nfForks

  input:
    set s, file(kmc) from kmcs1
  output:
	set s, file{"${s}*.bin1"} into bin1Fastqs

script: 
    // e.g., gonl-100a.fasta
    // todo: document this
	String dataset
	String id
	id = kmc.name.replaceFirst(kmcNameSuffix, "")
    """
    kmc2LocusAvg2.groovy -j ${kmc} -p ${probeFile} -e ${bin1Suffix} -i ${id} -o .

if ls *.bin1 1> /dev/null 2>&1; then
    : # noop
else
    echo "snp: " > "${id}_prediction.txt"

    touch "${id}_uninterpretable.bin1"
fi
    """
} // kmc2locusBin

/*
 * locusBin2ExtendedLocusBin
 * 
 * 1) Makes haplotype predictions from PA probes.
 *
 *
 * @todo document
 */
process locusBin2ExtendedLocusBin {
  publishDir resultDir, mode: 'copy', overwrite: true
  input:
		set s, file(b1List) from bin1Fastqs
  output:
	set s, file{"*_prediction.txt"} into predictionChannel

  script:
    """
    FILES="${s}*.bin1"
    outFile="${s}"
    outFile+="_prediction.txt"
    fileList=""
    id=""
    ext="*bin1*"
    for bFile in \$FILES; do
        if [ -s \$bFile ]; then
            if [[ \$bFile == \$ext ]]; then
                id=\$(basename "\$bFile")
                # '%' Means start to remove after the next character;
				# todo: change this to kmcNameSuffix
                id="\${id%%_*}"
                if [ "\$id" == "" ]; then
                    id=\$(basename "\$bFile")
                fi
                # echo \$bFile
                if [ "\$fileList" == "" ]; then
                    :
                else
                    fileList+=","
                fi
                fileList+=\$bFile
            fi
        fi
    done
    pa2Haps.groovy -a ${allOut} -h ${haps} -q "\$fileList" -o "\$outFile" -a ${params.allOut}
    """
} // locusBin2ExtendedLocusBin

// get the per-sample name
def sample(Path path) {
  def name = path.getFileName().toString()
  int start = Math.max(0, name.lastIndexOf('/'))
  int end = name.indexOf(kmcNameSuffix)
  if ( end <= 0 ) {
    throw new Exception( "Expected file " + name + " to end in '" + kmcNameSuffix + "'" );
  }
  return name.substring(start, end)
} // sample

workflow.onComplete {
  println "DONE: ${ workflow.success ? 'OK' : 'FAILED' }"
}

workflow.onError {
  println "ERROR: ${workflow.errorReport.toString()}"
}