{

  "par_general":
  {
    "outdir"              : "/scratch/carnold/CLL/TF_act_downsampling0.01/output",
    "regionExtension"     : 100,
    "analysisName"        : "CLL",
    "comparisonType"      : "CLL",
    "conditionComparison" : "mutated,unmutated",
    "designContrast"      : "~ Treatment + Condition",
 	"limit_nTF_to"        : -1
 },

"samples":
  {
    "summaryFile"      : "/scratch/carnold/CLL/TF_act_downsampling0.01/input/sampleTable_TF.tsv",
    "pairedEnd"        : true
  },


    "additionalInputFiles":
      {
        "peaks_bed"            : "/scratch/carnold/CLL/TF_act_downsampling0.01/input/CLL.consensus.5.bed",
        "refGenome_fasta"      : "/g/scb2/zaugg/zaugg_shared/annotations/hg19/referenceGenome/Bowtie2/hg19.fa",
        "dir_PWMScan"          : "/g/scb/zaugg/berest/ATACSeq/Analysis/Ackermann/HOCOMOCO.human/PWMscan"
      },

    "executables":
      {
        "volcanoPlot1_script"  : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/createVolcanoPlot.R",
        "prepareData_script"   : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/prepareData.R",
        "runTFAnalysis_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/runTFAnalysis.R",
        "consensusPeaks_script": "",
        "permutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/permutations.R",
		"summarizePermutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/summarizePermutations.R",
     	"preparePermutations_script" : "/g/scb2/zaugg/carnold/Projects/PWM_Ivan/src/R/preparePermutations.R"
	 }





}