rules.json

 {
    "rules": {
        "avia": ["wgslow","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","exomeseq-somatic"],
        "ngsqc": ["initialqc","initialqcgenomeseq"],
        "fastqc.fastq": ["initialqc","initialqcgenomeseq"],
        "bamstats": ["initialqc"],
        "fastq_screen": ["initialqc","initialqcgenomeseq"],
        "multiqc": ["initialqc"],
        "multiqc_genomeseq": ["initialqcgenomeseq"],
        "alview": ["exomeseq-somatic"],
#        "oncotator": ["exomeseq-somatic"],
        "oncotator_strelka": ["exomeseq-somatic"],
        "oncotator_mutect": ["exomeseq-somatic"],
#        "mutsig": ["exomeseq-somatic"],
        "mutsig_strelka": ["exomeseq-somatic"],
        "mutsig_mutect": ["exomeseq-somatic"],
        "mkdir_somatic": ["exomeseq-somatic"],
        "cnvkit_somatic": ["exomeseq-somatic"],
        "delly_somatic": ["exomeseq-somatic"],
        "fastqc.trimmed": ["initialqc","initialqcgenomeseq"],
        "trimmomatic": ["initialqc","initialqcgenomeseq"],
        "samtools.flagstats": ["none"],
        "samtools.flagstats.dedup": ["none"],
        "qualimap": ["initialqc"],
        "qualimap_wgs": ["initialqcgenomeseq"],
        "bwa.mem": ["initialqc","initialqcgenomeseq"],
        "novocraft.novoalign": ["none"],
        "bwa.index.ref": ["none"],
        "annovar": ["exomeseq-pairs"],
        "script.checkqc": ["none"],
        "samtools.sam2bam": ["none"],
        "script.coverage.qc": ["none"],
        "script.bzip2": ["none"],
        "picard.headers": ["initialqc","bam2recal","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","initialqcgenomeseq"],
        "picard.index.bam": ["none"],
        "picard.markdups": ["bam2recal","initialqc","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","initialqcgenomeseq"],
        "samtools.mpileup": ["none"],
        "gatk.realign": ["bam2recal","exomeseq-somatic","exomeseq-pairs","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow"],
        "gatk.recal": ["bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","exomeseq-somatic","exomeseq-germline"],
        "samtools.sort": ["none"],
        "novocraft.sort": ["bam2recal","initialqc","exomeseq-germline-partial","initialqcgenomeseq"],
        "varscan": ["exomeseq-pairs"],
        "gatk.genotype.gvcfs": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow"],
        "gatk.combine.gvcfs": ["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","wgslow"],
        "gatk.haplotype.caller.recal": ["exomeseq-germline-recal","exomeseq-germline-partial"],
        "snpeff": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial"],
        "snpeff_genomeseq": ["wgslow"],
        "snpeff.dbnsfp": ["none"],
        "script.split.gvcfs": ["none"],
        "mutect": ["exomeseq-somatic"],
#        "gatk.mutect2": ["exomeseq-somatic"],
#        "gatk.mutect2.chrom": ["exomeseq-somatic"],
        "strelka": ["exomeseq-somatic"],
        "make.somatic.network": ["exomeseq-somatic"],
        "make.germline.network": ["exomeseq-germline"],
        "make.genomeseq.network": ["wgslow"],
        "somatic.germline.calls": ["exomeseq-somatic"],
#        "gatk.merge.mutect2.chrom": ["exomeseq-somatic"],
        "gatk.merge.somatic.vcfs": ["exomeseq-somatic"],
        "snpeff_somatic": ["exomeseq-somatic"],
        "avia.make.bed.somatic": ["exomeseq-somatic"],
        "avia.make.bed.germ": ["exomeseq-germline"],
        "avia.make.bed.genomeseq": ["wgslow"],
        "database_germline": ["exomeseq-germline"],
        "database_genomeseq": ["wgslow"],
        "database_somatic": ["exomeseq-somatic"],
        "svdetect": ["none"],
        "bicseq": ["none"],
        "generate_QC_table": ["initialqc"],
        },
    "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",
        "exomeseq-germline-recal": "all-exomeseq-germline-realign.rl",
        "initialqc": "all-initialqc.rl",
        "initialqcgenomeseq": "all-initialqcgenomeseq.rl",
        "bam2recal": "all-bam2recal.rl",
        "custom": "all-custom.rl",
	"rnaseq": "rnaseq.snakefile",
	"initialqcrnaseq": "initialqcrnaseq.snakefile",
	"CAPmirseq-plus": "CAPmirseq-plus.snakefile",	
        }

 }