exome.2/project.json at master · DLWheeler/exome.2 · GitHub

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 {
        "project": {
             "id": "hg-chr21+22-test",
             "analyst": "C. Darwin",
             "pi": "na",
             "poc": "na",
             "organism": "Homo sapiens",
             "pipeline": "test",
             "version": "1.0"
        },
        "references": {
             "GENOME": "/ngs/Sequence/reference/human/hg18/bundle/chr21+22.fasta",
             "INDELSITES": "/ngs/Sequence/reference/human/hg18/bundle/Mills_and_1000G_gold_standard.indels.hg18.vcf",
             "NOVOINDEX": "/ngs/Sequence/reference/human/hg18/bundle/human_g1k_v37_iupac.nix",
             "REFFLAT": "/ngs/Sequence/reference/hg18/bundle/SureSelect/SS_exome.txt",
             "SNPSITES": "/ngs/Sequence/reference/human/hg18/bundle/dbsnp_138.hg18.vcf"
        },
        "samples": {
            "hs1": ["normal"],
            "hs2": ["tumor"]
        },
        "pairs": {
            "hs1+hs2": ["hs1","hs2"]
        },

        "platform": "Illumina",
        "mapping_params": {
            "default": ""
        },
        "bin": {
             "BWA": "/home/david/Builds/bwa-0.7.10/bwa",
             "ANNOVAR1": "/ngs/bin/annovar/convert2annovar.pl",
             "ANNOVAR2": "/ngs/bin/annovar/table_annovar.pl",
             "COVCALC": "/ngs/bin/Coverage_calc4.pl",
             "COVFREQ": "/ngs/bin/Cov_Frequency3.R",
             "GATK": "/ngs/bin/java -Xmx2g -jar /ngs/bin/Gatk/GenomeAnalysisTK.jar",
             "MARKDUPS": "picard-tools MarkDuplicates",
             "PICARD1": "picard-tools AddOrReplaceReadGroups",
             "PICARD2": "picard-tools CollectInsertSizeMetrics",
             "PICHIST": "/ngs/bin/picardhist.R",
             "QCAL": "/ngs/bin/qcalplot.R",
             "READDIST": "/ngs/bin/ReadDist.R",
             "VARSCAN": "java -jar /ngs/bin/VarScan.v2.3.7.jar"
        },
        "paths": {
            "ANNDIR": "/ngs/bin/annovar/humandb/"
        },
        "constants": {
            "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
            "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT"
        },
    "rules": {
        "map_pe":["exomeseq-pairs"],
        "index_ref":["exomeseq-pairs"],
        "annovar":["exomeseq-pairs"],
        "checkqc":["exomeseq-pairs"],
        "sam2bam":["exomeseq-pairs"],
        "flagstats":["exomeseq-pairs"],
        "flagstats_dedup":["exomeseq-pairs"],
        "coverage_qc":["exomeseq-pairs"],
        "headers":["exomeseq-pairs"],
        "markdups":["exomeseq-pairs"],
        "mpileup":["exomeseq-pairs"],
        "realign":["exomeseq-pairs"],
        "recal":["exomeseq-pairs"],
        "sam2bam":["exomeseq-pairs"],
        "sort":["exomeseq-pairs"],
        "varscan":["exomeseq-pairs"]
        },
    "final": {
        "exomeseq-pairs": "Rules/all-exomeseq-pairs.rl"
        }

 }