panelCapture_inputs.json

{
  "panelCapture.compressIndexVcfDv.VcfExtension": "String (optional, default = \"vcf\")",
  "panelCapture.vcfPolyXJar": "String",
  "panelCapture.sambambaExe": "String",
  "panelCapture.tabixExe": "String",
  "panelCapture.genomeVersion": "String",
  "panelCapture.refSa": "File",
  "panelCapture.knownSites3": "File",
  "panelCapture.knownSites3Index": "File",
  "panelCapture.hcSuffix": "String (optional, default = \".hc\")",
  "panelCapture.intervalBedFile": "File",
  "panelCapture.minCovBamQual": "Int",
  "panelCapture.variantEvalEV": "String (optional, default = \"MetricsCollection\")",
  "panelCapture.bgZipExe": "String",
  "panelCapture.memoryLow": "Int",
  "panelCapture.debug": "Boolean (optional, default = false)",
  "panelCapture.refAmb": "File",
  "panelCapture.suffix1": "String",
  "panelCapture.refDict": "File",
  "panelCapture.modelType": "String",
  "panelCapture.referenceFasta": "String",
  "panelCapture.bedtoolsLowCoverage": "Int",
  "panelCapture.singularity": "String",
  "panelCapture.gatkExe": "String",
  "panelCapture.knownSites2Index": "File",
  "panelCapture.refFaiGz": "File",
  "panelCapture.bcfToolsExe": "String",
  "panelCapture.workflowType": "String",
  "panelCapture.crumbleExe": "String",
  "panelCapture.fastqR1": "File",
  "panelCapture.bwaExe": "String",
  "panelCapture.memoryHigh": "Int",
  "panelCapture.outDir": "String",
  "panelCapture.compressIndexVcf.VcfExtension": "String (optional, default = \"vcf\")",
  "panelCapture.sampleID": "String",
  "panelCapture.refFasta": "File",
  "panelCapture.fastqR2": "File",
  "panelCapture.cpuHigh": "Int",
  "panelCapture.bedToolsSmallInterval": "Int",
  "panelCapture.knownSites1Index": "File",
  "panelCapture.vcftoolsExe": "String",
  "panelCapture.dvSuffix": "String (optional, default = \".dv\")",
  "panelCapture.compressIndexVcfHc.VcfExtension": "String (optional, default = \"vcf\")",
  "panelCapture.toolVersions.dollar": "String (optional, default = \"$\")",
  "panelCapture.subdivisionMode": "String",
  "panelCapture.sedExe": "String",
  "panelCapture.qualimapExe": "String",
  "panelCapture.refFai": "File",
  "panelCapture.awkExe": "String",
  "panelCapture.bedFile": "String",
  "panelCapture.refBwt": "File",
  "panelCapture.knownSites1": "File",
  "panelCapture.ldLibraryPath": "String",
  "panelCapture.refData": "String",
  "panelCapture.cpuLow": "Int",
  "panelCapture.refPac": "File",
  "panelCapture.bcftoolsNormDv.VcfExtension": "String (optional, default = \"vcf\")",
  "panelCapture.bedToolsExe": "String",
  "panelCapture.fastqcExe": "String",
  "panelCapture.samtoolsExe": "String",
  "panelCapture.data": "String",
  "panelCapture.swMode": "String",
  "panelCapture.suffix2": "String",
  "panelCapture.outputMnt": "String",
  "panelCapture.javaExe": "String",
  "panelCapture.sortExe": "String",
  "panelCapture.dvOut": "String",
  "panelCapture.multiqcExe": "String",
  "panelCapture.refAnn": "File",
  "panelCapture.knownSites2": "File",
  "panelCapture.refFastaGz": "File",
  "panelCapture.mergeVCFMobiDL": "File",
  "panelCapture.platform": "String",
  "panelCapture.refFaiGzi": "File",
  "panelCapture.emitRefConfidence": "String (optional, default = \"NONE\")",
  "panelCapture.deepExe": "String",
  "panelCapture.bcftoolsNormHc.VcfExtension": "String (optional, default = \"vcf\")",
  "panelCapture.singularityImg": "String"
}