config.json

{
	"sampleInfo" : "sampleInfo.tsv",
	"sampleInfoDelimiter" : "\t",
	"baseNameColumns" : ["sample", "rep"],
	"poolBaseNameColumns" : ["sample"],
	"refGenome" : "dm6",
	"spikeGenome" : "sacCer3",
	"readLen" : 75,
	"genome" : {
		"dm3" : { 
			"bowtie" : "/proj/mckaylab/genomeFiles/dm3/RefGenome/dm3",
			"fasta" : "",
			"chrSize" : "/proj/mckaylab/genomeFiles/dm3/dm3.chrom.sizes",
			"controlDNAPath" : "/proj/mckaylab/genomeFiles/dm3/ControlGenomicDNA/ControlGenomicDNA_q5_sorted_dupsRemoved_noYUHet.bed",
			"genomeSize" : 121400000
		},
		"dm6" : { 
			"bowtie" : "/proj/mckaylab/genomeFiles/dm6/Bowtie2Index/genome",
			"fasta" : "/proj/mckaylab/genomeFiles/dm6/dm6.fa",
			"chrSize" : "/proj/mckaylab/genomeFiles/dm6/dm6_chromSizes.txt",
			"controlDNAPath" : "/proj/mckaylab/genomeFiles/dm6/ControlGenomicDNA/ControlGenomicDNA_trim_q5_dupsRemoved.bed",
			"genomeSize" : 137547960
		},
		"ecoli" : { 
			"bowtie" : "/proj/mckaylab/genomeFiles/Ecoli_K12_DH10B_ENSEMBL/Bowtie2Index/genome",
			"fasta" : "/proj/mckaylab/genomeFiles/Ecoli_K12_DH10B_ENSEMBL/ecoli.fa"
		},
		"sacCer3" : { 
			"bowtie" : "/proj/mckaylab/genomeFiles/sacCer3/Bowtie2Index/genome",
			"fasta" : "/proj/mckaylab/genomeFiles/sacCer3/sacCer3.fa"
		},
		"droYak2" : {
			"bowtie" : "/proj/mckaylab/genomeFiles/droYak2/RefGenome/droYak2",
			"fasta" : "/proj/mckaylab/genomeFiles/droYak2/droYak2.fa"
		}
	},
	"module" : {
		"bbmapVer" : "bbmap/38.71",
		"bowtie2Ver" : "bowtie2/2.3.4.1",
		"samtoolsVer" : "samtools/1.10",
		"picardVerNum" : "2.2.4",
		"picardVer" : "picard/2.2.4",
		"picardPath" : "/nas/longleaf/apps/picard/2.2.4/picard-tools-2.2.4/picard.jar",
		"bedtoolsVer" : "bedtools/2.26",
		"ucscVer" : "ucsctools/320",
		"macsVer" : "macs/2.1.2",
		"rVer" : "r/4.1.3",
		"fastqcVer" : "fastqc/0.11.7",
		"multiqcVer" : "multiqc/1.7",
		"deeptoolsVer" : "deeptools/2.4.1",
		"pythonVer" : "python/3.5.1",
		"fqscreenPath" : "/proj/mckaylab/genomeFiles/fastq_screen_v0.11.1/fastq_screen",
		"fqscreenConf" : "/proj/mckaylab/genomeFiles/fastq_screen.conf",
		"mlrPath" : "/proj/mckaylab/bin/mlr"
	}
}