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rules.json
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rules.json
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{
"rules": {
"avia": ["wgslow","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","rnaseqvargerm"],
"rnaseqforfusions": ["rnaseqfusion"],
"rnafusioncleanup": ["none"],
"vcf2maf": ["exomeseq-somatic","wgs-somatic"],
"vcf2maf_tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
"maftools": ["exomeseq-somatic","wgs-somatic"],
"maftools_tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
"germline_filter_wgs": ["wgslow"],
"delly_germline": ["wgslow"],
"pindel_germline": ["none"],
"canvas_wgs_germ": ["wgslow"],
"canvas_wgs_somatic": ["wgs-somatic"],
"canvas_wgs_tumoronly": ["wgs-somatic-tumoronly"],
"svaba_germline": ["wgslow"],
"svaba_wgs_somatic": ["wgs-somatic"],
"breakdancer_germline": ["wgslow"],
"gatk.genotype.somatic.gvcfs": ["exomeseq-somatic","exomeseq-somatic-tumoronly","wgs-somatic","wgs-somatic-tumoronly"],
"gatk.combine.somatic.gvcfs": ["exomeseq-somatic","exomeseq-somatic-tumoronly","wgs-somatic","wgs-somatic-tumoronly"],
"script.somatic.batchgvcf": ["exomeseq-somatic","exomeseq-somatic-tumoronly","wgs-somatic","wgs-somatic-tumoronly"],
"manta_germline": ["exomeseq-germline"],
"manta_wgs_somatic": ["wgs-somatic"],
"manta_somatic": ["exomeseq-somatic"],
"manta_somatic_tumoronly": ["exomeseq-somatic-tumoronly"],
"manta_wgs_somatic_tumoronly": ["wgs-somatic-tumoronly"],
"manta_wgs": ["wgslow"],
"germline_filter_exome": ["exomeseq-germline"],
"gatk_select_variants": ["exomeseq-germline"],
"gatk_select_variants_genomeseq": ["wgslow"],
"gatk_select_variants_rnaseqvar": ["rnaseqvargerm"],
"gatk.merge.chrom": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
"ngsqc": ["initialqc","initialqcgenomeseq","rnaseqvargerm"],
"fastqc.fastq": ["initialqc","initialqcgenomeseq"],
"fastqc.rnaseqvar": ["rnaseqvargerm","rnaseqfusion"],
"bamstats": ["initialqc"],
"make_target_files": ["initialqc","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-germline"],
"fastq_screen": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"],
"multiqc": ["initialqc"],
"multiqc_genomeseq": ["initialqcgenomeseq"],
"alview": ["exomeseq-somatic"],
"oncotator_strelka": ["none"],
"oncotator_mutect": ["none"],
"oncotator_mutect2": ["none"],
"mutsig_strelka": ["exomeseq-somatic","wgs-somatic"],
"mutsig_mutect": ["exomeseq-somatic","wgs-somatic"],
"mutsig_mutect2": ["exomeseq-somatic","wgs-somatic"],
"mutsig_mutect2_tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
"mkdir_somatic": ["exomeseq-somatic","wgs-somatic"],
"mkdir_somatic_tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
"rnafusionmkdir": ["rnaseqfusion"],
"starfusion": ["rnaseqfusion"],
"fusioncatcher": ["rnaseqfusion"],
"fusioninsp_starfus": ["rnaseqfusion"],
"fusioninsp_fuscatch": ["rnaseqfusion"],
"oncofuse_fuscatch": ["rnaseqfusion"],
"oncofuse_starfus": ["rnaseqfusion"],
"cnvkit_somatic": ["exomeseq-somatic"],
"cnvkit_germ": ["none"],
"cnvkit_wgs_somatic": ["wgs-somatic"],
"cnvkit_summary": ["exomeseq-somatic","wgs-somatic"],
"cnvkit_somatic_tumoronly": ["exomeseq-somatic-tumoronly"],
"cnvkit_summary_tumoronly": ["exomeseq-somatic-tumoronly"],
"delly_somatic": ["exomeseq-somatic","wgs-somatic"],
"fastqc.trimmed": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"],
"trimmomatic": ["initialqc","initialqcgenomeseq","rnaseqvargerm","rnaseqfusion"],
"samtools.flagstats": ["none"],
"samtools.flagstats.dedup": ["none"],
"qualimap_rnaseqvar": ["rnaseqvargerm"],
"qualimap_wgs": ["initialqcgenomeseq"],
"qualimap": ["initialqc"],
"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": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-pairs","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
"gatk.recal": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-germline","rnaseqvargerm"],
"samtools.sort": ["none"],
"novocraft.sort": ["bam2recal","initialqc","exomeseq-germline-partial","initialqcgenomeseq","rnaseqvargerm"],
"varscan": ["exomeseq-pairs"],
"gatk.genotype.gvcfs": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
"gatk.combine.gvcfs": ["exomeseq-germline-recal","exomeseq-germline-partial","exomeseq-germline","rnaseqvargerm"],
"script.batchgvcf": ["exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","rnaseqvargerm"],
"gatk.variant.annotator": ["none"],
"gatk.apply.variant.recal": ["none"],
"gatk.splitncigarreads": ["rnaseqvargerm"],
"gatk.rnaseqvar.haplotype.caller": ["rnaseqvargerm"],
"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"],
"mutect_wgs": ["wgs-somatic"],
"gatk.mutect2": ["exomeseq-somatic","wgs-somatic"],
"gatk.mutect2.tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
"strelka": ["exomeseq-somatic"],
"wgs_strelka": ["wgs-somatic"],
"make.somatic.network": ["exomeseq-somatic","exomeseq-somatic-tumoronly"],
"make.wgs.somatic.network": ["wgs-somatic","wgs-somatic-tumoronly"],
"admixture_germline": ["exomeseq-germline"],
"admixture_somatic": ["exomeseq-somatic","exomeseq-somatic-tumoronly"],
"admixture_wgs_somatic": ["wgs-somatic","wgs-somatic-tumoronly"],
"admixture_wgs": ["wgslow","rnaseqvargerm"],
"make.germline.network": ["exomeseq-germline"],
"make.genomeseq.network": ["wgslow","rnaseqvargerm"],
"somatic.germline.calls": ["exomeseq-somatic","exomeseq-somatic-tumoronly"],
"wgs.somatic.germline.calls": ["wgs-somatic","wgs-somatic-tumoronly"],
"gatk.merge.mutect2.chrom": ["exomeseq-somatic"],
"gatk.merge.wgs.mutect2.chrom": ["wgs-somatic"],
"gatk.merge.wgs.mutect2.chrom.tumoronly": ["wgs-somatic-tumoronly"],
"gatk.merge.mutect2.chrom.tumoronly": ["exomeseq-somatic-tumoronly"],
"gatk.merge.somatic.vcfs": ["none"],
"snpeff_somatic": ["none"],
"avia.make.bed.somatic": ["none"],
"avia.make.bed.germ": ["exomeseq-germline"],
"avia.make.bed.genomeseq": ["wgslow"],
"avia.make.bed.rnaseqvar": ["rnaseqvargerm"],
# "database_germline": ["exomeseq-germline"],
# "database_genomeseq": ["wgslow"],
"database_somatic": ["exomeseq-somatic","wgs-somatic"],
"database_somatic_tumoronly": ["wgs-somatic-tumoronly","exomeseq-somatic-tumoronly"],
"svdetect": ["none"],
"bicseq": ["none"],
"generate_QC_table": ["none"],
"star.align": ["rnaseqvargerm"],
"star.align.2": ["rnaseqvargerm"],
"picard.rnaseqvar.headers": ["rnaseqvargerm"],
"picard.rnaseqvar.markdups": ["rnaseqvargerm"],
"germline_filter_rnaseqvar": ["rnaseqvargerm"],
"conpair": ["exomeseq-somatic","wgs-somatic"],
"theta": ["exomeseq-somatic","wgs-somatic"]
},
"final": {
"exomeseq-pairs": "all-exomeseq-pairs.rl",
"wgslow": "all-wgslow.rl",
"wgs-somatic": "all-wgs-somatic.rl",
"wgs-somatic-tumoronly": "all-wgs-somatic-tumoronly.rl",
"exomeseq-somatic": "all-exomeseq-somatic.rl",
"exomeseq-somatic-tumoronly": "all-exomeseq-somatic-tumoronly.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",
"rnaseqvargerm": "all-rnaseqvargerm.rl",
"rnaseqfusion": "all-rnafusion.rl",
# "rnaseqvar-germline": "all-rnaseqvar-germline.rl",
# "rnaseqvar-somatic": "all-rnaseqvar-somatic.rl",
"rnaseq": "rnaseq.snakefile",
"initialqcrnaseq": "initialqcrnaseq.snakefile",
"cellranger": "scrnaseq.snakefile",
"scrnaseqinit": "scrnaseq.snakefile",
"scrnaseqcluster": "scrnaseq.snakefile",
"CAPmirseq-plus": "CAPmirseq-plus.snakefile",
"InitialChIPseqQC":"InitialChIPseqQC.snakefile",
"ChIPseq":"ChIPseq.snakefile",
}
}