canFam3.json

{
 	"references": {
 		"exomeseq": {},
 		"genomeseq": {},
 		"rnaseq": {
 			"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/canFam3.fa",
 			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/genes.gtf",
			"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/qualimap_info.txt",
                        "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/karyoplot_gene_coordinates.txt",
 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.7.0f/genes-",
 			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/annotate.genes.txt",
 			"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/annotate.isoforms.txt",
 			"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/refFlat.txt",
 			"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/genes.ref.bed",
 			"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/geneinfo.bed",
 			"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/camFam/",
 			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/rsemref/canFam3",
 			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/canFam3.rRNA_interval_list",
 			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.7.0f/genes-",
 			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
 			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/canFam3.fa",
 			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
 			"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
 			"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
 			"ORGANISM": "Canis_lupus_familiaris"
 		},
 		"rnaseqvargerm": {},
 		"ChIPseq": {}
	}
}