mm10_M29.json

{
    "references": {
        "exomeseq": {},
        "genomeseq": {},
        "rnaseq": {
            "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.fa",
            "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.fa",
            "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/GTFs/mm10/gencode.vM25.annotation.gtf",
            "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/STAR/2.7.0f/genes-",
            "STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/STAR/2.7.0f/genes-",
            "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/annotate.genes.txt",
            "ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/annotate.isoforms.txt",
            "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/refFlat.txt",
            "BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/genes.ref.bed",
            "GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/geneinfo.bed",
            "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/qualimap_info.txt",
            "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/karyobeds/",
            "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/karyoplot_gene_coordinates.txt",
            "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/rsemref/mm10_M29",
            "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_M29/mm10_M29.rRNA_interval_list",
            "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
            "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
            "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
            "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
            "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
            "ORGANISM": "CUSTOM"
        },
        "rnaseqvargerm": {},
        "ChIPseq": {}
    }
}