rules.json~

 {
    "rules": {
        "avia": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "ngsqc": ["initialqc","wgslow"],
        "fastqc.fastq": ["initialqc","wgslow"],
        "fastqc.trimmed": ["initialqc","wgslow"],
        "trimmomatic": ["initialqc","wgslow"],
	"samtools.flagstats": ["none"],
	"samtools.flagstats.dedup": ["none"],
        "qualimap": ["initialqc","wgslow"],
        "bwa.mem":["wgslow","initialqc"],
        "novocraft.novoalign":["none"],
        "bwa.index.ref":["none"],
        "annovar":["exomeseq-pairs"], 
        "script.checkqc":["exomeseq-pairs","exomeseq-somatic","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "samtools.sam2bam":["initialqc","wgslow"], 
        "script.coverage.qc":["none"],
        "script.bzip2":["none"],         
        "picard.headers":["initialqc","bam2recal","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow"], 
        "picard.index.bam":["none"],
        "picard.markdups":["bam2recal","initialqc","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow"], 
        "samtools.mpileup":["exomeseq-pairs"], 
        "gatk.realign":["bam2recal","exomeseq-somatic","exomeseq-pairs","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"], 
        "gatk.recal":["bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial"], 
        "samtools.sort":["none"],
        "novocraft.sort":["bam2recal","initialqc","exomeseq-germline-partial","wgslow"],         
        "varscan":["exomeseq-pairs"],
        "gatk.genotype.gvcfs":["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "gatk.combine.gvcfs":["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "script.batchgvcf":["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "gatk.variant.annotator":["none"],
        "gatk.apply.variant.recal":["none"],
        "gatk.variant.recal":["none"],
        "gatk.haplotype.caller":["exomeseq-germline"],
        "gatk.haplotype.caller.recal":["exomeseq-germline-recal","exomeseq-germline-partial"],        
        "snpeff": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "snpeff.dbnsfp": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "script.split.gvcfs": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "mutect": ["none"],
        "mutect2": ["exomeseq-somatic"],
        "svdetect": ["none"],
        "bicseq": ["none"]
        },
    "final": {
        "exomeseq-pairs": "all-exomeseq-pairs.rl",
        "wgslow": "all-wgslow.rl",
        "exomeseq-somatic": "all-exomeseq-somatic.rl",
	"exomeseq-germline": "all-exomeseq-germline.rl",
        "exomeseq-germline-partial": "all-exomeseq-germline-partial.rl",
	"initialqc": "all-initialqc.rl",
        "bam2recal": "all-bam2recal.rl",
        "custom": "all-custom.rl"        
        }

 }