diff --git a/gatk.wdl b/gatk.wdl index c1cb9480b80ceb8816eabd9ddb32c146e4117f9d..8e67edc850da41a988bc064202f2313e3dc2548a 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -1553,8 +1553,8 @@ task SplitNCigarReads { task VariantEval { input { - Array[File] inputVcfs - Array[File] inputVcfsIndex + Array[File] evalVcfs + Array[File] evalVcfsIndex Array[File] comparisonVcfs = [] Array[File] comparisonVcfsIndex = [] File? referenceFasta @@ -1574,7 +1574,7 @@ task VariantEval { String memory = "5G" String javaXmx = "4G" # TODO: Refine estimate. For now 4 minutes per GB of input. - Int timeMinutes = ceil(size(flatten([inputVcfs, comparisonVcfs]), "G") * 4) + Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs]), "G") * 4) String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0" } @@ -1584,7 +1584,7 @@ task VariantEval { gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \ VariantFiltration \ -O ~{outputPath} \ - ~{true="--eval" false="" length(inputVcfs) > 0} ~{sep=" --eval " inputVcfs} \ + ~{true="--eval" false="" length(evalVcfs) > 0} ~{sep=" --eval " evalVcfs} \ ~{true="--comparison" false="" length(comparisonVcfs) > 0} ~{sep=" --comparison " comparisonVcfs} \ ~{"-R " + referenceFasta} \ ~{"--dbsnp " + dbsnpVCF } \ @@ -1609,12 +1609,22 @@ task VariantEval { time_minutes: timeMinutes } parameter_meta { + evalVcfs: {description: "Variant sets to evaluate." category: "required"} + evalVcfsIndex: {description: "Indexes for the variant sets.", category: "required"} + comparisonVcfs: {description: "Compare set vcfs.", category: "advanced"} + comparisonVcfsIndex: {description: "Indexes for the compare sets.", category: "advanced"} + evalModules: {description: "One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless doNotUseAllStandardModules=true)", category: "common"} + stratificationModules: {description: "One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless doNotUseAllStandardStratifications=true)", category: "common"} + samples: {description: "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context." , category: "advanced"} # Advanced because this description is impossible to understand... + mergeEvals: {description: "If provided, all evalVcf tracks will be merged into a single eval track", category: "common"} + doNotUseAllStandardModules: {description: "Do not use the standard modules by default (instead, only those that are specified with the evalModules option).", category: "common"} + doNotUseAllStandardStratifications: {description: "Do not use the standard stratification modules by default (instead, only those that are specified with the stratificationModules option).", category: "common"} referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "common"} referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "common"} referenceFastaFai: {description: "The index for the reference fasta file.", category: "common"} dbsnpVCF: {description: "A dbSNP VCF.", category: "common"} dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"} - outputPath: {description: "The location the output table should be written.", category: "common"} + outputPath: {description: "The location the output table should be written.", category: "advanced"} memory: {description: "The amount of memory this job will use.", category: "advanced"} javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}