From c58cf2183ef7d821f1454ee8093b7a60d2141b1f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 28 May 2020 15:17:16 +0200
Subject: [PATCH] add variant eval parameter_meta
---
gatk.wdl | 20 +++++++++++++++-----
1 file changed, 15 insertions(+), 5 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index c1cb948..8e67edc 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"}
--
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