From 0b2a14fcc25b6dfc1617cc4253577512ea4dacb3 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 8 Jan 2020 17:59:17 +0100
Subject: [PATCH] add parameter_meta to BaseRecibrator
---
gatk.wdl | 26 ++++++++++++++++++++++++--
picard.wdl | 12 ++++++------
2 files changed, 30 insertions(+), 8 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 04112be..144d573 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -51,7 +51,7 @@ task ApplyBQSR {
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
- sequenceGroupInterval: {description: "The regions to operate on", category: "advanced"}
+ sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
@@ -59,7 +59,7 @@ task ApplyBQSR {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -108,6 +108,28 @@ task BaseRecalibrator {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
+ inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
+ recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"}
+ sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advancded"}
+ knownIndelsSitesVCFs: {description: "VCf files with known indels.", category: "advanced"}
+ knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs", category: "advanced"}
+ dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
+ dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.",
+ category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+
+ 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"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
}
task CombineGVCFs {
diff --git a/picard.wdl b/picard.wdl
index e7f494f..bc6f464 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -36,7 +36,7 @@ task BedToIntervalList {
outputPath: {description: "The location the output interval list should be written to.",
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -164,7 +164,7 @@ task CollectMultipleMetrics {
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -217,7 +217,7 @@ task CollectRnaSeqMetrics {
category: "common"}
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -282,7 +282,7 @@ task CollectTargetedPcrMetrics {
category: "required"}
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -329,7 +329,7 @@ task GatherBamFiles {
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -371,7 +371,7 @@ task GatherVcfs {
outputVcfPath: {description: "The path where the merged VCF file will be written.", caregory: "required"}
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.",
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
--
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