test.json 1.75 KB
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{
    "referenceFile" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
    "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
    "samtools": { "exe": "test"},
    "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
    "star" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
    "bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
    "flexiprep": {
        "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
        "sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
    },
    "mapping": {
    },
    "gatk": {
        "mapping": {
            "flexiprep": {
            }
        },
        "referenceFile" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
        "dbsnp": "/home/pjvan_thof/pipelines/test/test",
        "hapmap": "/home/pjvan_thof/pipelines/test/test",
        "omni": "/home/pjvan_thof/pipelines/test/test",
        "1000G": "/home/pjvan_thof/pipelines/test/test",
        "mills": "/home/pjvan_thof/pipelines/test/test",
        "haplotypecaller": {
            "stand_call_conf": 20,
            "stand_emit_conf": 20
        }
    },
    "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
    "samples": {
        "test": {
            "ID": "test",
            "runs": {
                "1" : {
                    "ID": "1",
                    "R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
                    "R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
                },
                "2" : {
                    "ID": "1",
                    "R1" : "/home/pjvan_thof/pipelines/test/test.R1.fastq.gz",
                    "R2" : "/home/pjvan_thof/pipelines/test/test.R2.fastq.gz"
                }
            }
        }
    }
}