{

      "par_general":
      {
        "indir": "/scratch/daga/Psoriasis_SLE/Psoriasis_SLE_all_batches/Psoriasis_SLE_seq_all_rounds_last/Fastq_sym_links",
        "outdir" : "/scratch/daga/Psoriasis_SLE/Psoriasis_SLE_all_batches/Psoriasis_SLE_seq_all_rounds_last"
      },

      "wildcard_pattern":
      {
        "fastq_input" : "_fastq.gz" ,
        "fastqc_bt" : "_fastq_fastqc.zip",
        "fastq_trim": "_trimmed_fastq.gz",
        "fastqc_at" : "_trimmed_fastq_fastqc.zip"
      },

    "executables":
      {
        "java_exec"       : "java-8",
        "bowtie2_exec"    : "bowtie2",
        "Trimmomatic_exec": "/g/scb/zaugg/daga/miniconda3/share/trimmomatic-0.36-5/trimmomatic.jar",
        "fastqc_exec"     : "fastqc",
        "samtools_exec"   : "samtools",
        "picardtoolsJar"  : "/g/scb/zaugg/daga/miniconda3/share/picard-2.17.6-0/picard.jar",
        "macs2_exec"       : "macs2"
      },
    "additionalInputFiles":
      {
        trim_adaptor_file : "/g/scb/zaugg/daga/miniconda3/share/trimmomatic-0.36-5/adapters/TruSeq3-SE.fa"

      },

    "par_trimming":
      {
        "trimmomatic_mode"  : "SE",
        "trimmomatic_ILLUMINACLIP"  : "2:30:10",
        "trimmomatic_trailing"      : 3,
        "trimmomatic_leading"       : 3,
        "trimmomatic_minlen"        : 36,
        "trimmomatic_sliding_window" : "4:15",
        "trimmomatic_adapters" : "/g/scb/zaugg/daga/miniconda3/share/trimmomatic-0.36-5/adapters/TruSeq3-SE.fa"

      },

    "par_align":
    {
        "bowtie2_sensitivity"   : "--very-sensitive",
        "bowtie2_refGenome"     : "/g/scb2/zaugg/zaugg_shared/annotations/hg38/referenceGenome/Bowtie2/hg38"

      },

    "par_postalign":
    {
        "minMAPQscore"                       : 10,
        "ValidationStringencySortSam"        : "LENIENT",
        "ValidationStringencyMarkDuplicates" : "SILENT"
      }



}