From 0e6bde497f1a239692783c5e90c69bc38442f7de Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:29:14 +0200
Subject: [PATCH] gatk to 1.0
---
gatk.wdl | 296 +++++++++++++++++++++++++++++--------------------------
1 file changed, 155 insertions(+), 141 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index fbbc813..e6c530e 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1,19 +1,22 @@
+version 1.0
# Apply Base Quality Score Recalibration (BQSR) model
task ApplyBQSR {
- String? preCommand
- File? gatkJar
- File inputBam
- File inputBamIndex
- String outputBamPath
- File recalibrationReport
- Array[File]+ sequenceGroupInterval
- File refDict
- File refFasta
- File refFastaIndex
- Int? compressionLevel
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File? gatkJar
+ File inputBam
+ File inputBamIndex
+ String outputBamPath
+ File recalibrationReport
+ Array[File]+ sequenceGroupInterval
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Int? compressionLevel
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -23,18 +26,18 @@ task ApplyBQSR {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
- -R ${refFasta} \
- -I ${inputBam} \
+ -R ~{refFasta} \
+ -I ~{inputBam} \
--use-original-qualities \
- -O ${outputBamPath} \
- -bqsr ${recalibrationReport} \
+ -O ~{outputBamPath} \
+ -bqsr ~{recalibrationReport} \
--static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
- -L ${sep=" -L " sequenceGroupInterval}
+ -L ~{sep=" -L " sequenceGroupInterval}
}
output {
@@ -49,19 +52,23 @@ task ApplyBQSR {
# Generate Base Quality Score Recalibration (BQSR) model
task BaseRecalibrator {
- String? preCommand
- File? gatkJar
- File inputBam
- File inputBamIndex
- String recalibrationReportPath
- Array[File]+ sequenceGroupInterval
- Array[File]? knownIndelsSitesVCFs
- Array[File]? knownIndelsSitesIndices
- File? dbsnpVCF
- File? dbsnpVCFindex
- File refDict
- File refFasta
- File refFastaIndex
+ input {
+ String? preCommand
+ File? gatkJar
+ File inputBam
+ File inputBamIndex
+ String recalibrationReportPath
+ Array[File]+ sequenceGroupInterval
+ Array[File]? knownIndelsSitesVCFs
+ Array[File]? knownIndelsSitesIndices
+ File? dbsnpVCF
+ File? dbsnpVCFindex
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Float? memory
+ Float? memoryMultiplier
+ }
Array[File]+ knownIndelsSitesVCFsArg = flatten([
select_first([knownIndelsSitesVCFs, []]),
@@ -72,9 +79,6 @@ task BaseRecalibrator {
select_all([dbsnpVCFindex])
])
- Float? memory
- Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
@@ -83,15 +87,15 @@ task BaseRecalibrator {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
BaseRecalibrator \
- -R ${refFasta} \
- -I ${inputBam} \
+ -R ~{refFasta} \
+ -I ~{inputBam} \
--use-original-qualities \
- -O ${recalibrationReportPath} \
- --known-sites ${sep=" --known-sites " knownIndelsSitesVCFsArg} \
- -L ${sep=" -L " sequenceGroupInterval}
+ -O ~{recalibrationReportPath} \
+ --known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
+ -L ~{sep=" -L " sequenceGroupInterval}
}
output {
@@ -104,22 +108,24 @@ task BaseRecalibrator {
}
task CombineGVCFs {
- String? preCommand
- Array[File]+ gvcfFiles
- Array[File]+ gvcfFileIndexes
- Array[File]+ intervals
+ input {
+ String? preCommand
+ Array[File]+ gvcfFiles
+ Array[File]+ gvcfFileIndexes
+ Array[File]+ intervals
- String outputPath
+ String outputPath
- String? gatkJar
+ String? gatkJar
- File refFasta
- File refFastaIndex
- File refDict
+ File refFasta
+ File refFastaIndex
+ File refDict
- Int? compressionLevel
- Float? memory
- Float? memoryMultiplier
+ Int? compressionLevel
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -129,18 +135,18 @@ task CombineGVCFs {
command {
set -e -o pipefail
- ${preCommand}
+ ~{preCommand}
- if [ ${length(gvcfFiles)} -gt 1 ]; then
- ${toolCommand} \
+ if [ ~{length(gvcfFiles)} -gt 1 ]; then
+ ~{toolCommand} \
CombineGVCFs \
- -R ${refFasta} \
- -O ${outputPath} \
- -V ${sep=' -V ' gvcfFiles} \
- -L ${sep=' -L ' intervals}
+ -R ~{refFasta} \
+ -O ~{outputPath} \
+ -V ~{sep=' -V ' gvcfFiles} \
+ -L ~{sep=' -L ' intervals}
else # TODO this should be handeled in wdl
- ln -sf ${select_first(gvcfFiles)} ${outputPath}
- ln -sf ${select_first(gvcfFileIndexes)} ${outputPath}.tbi
+ ln -sf ~{select_first(gvcfFiles)} ~{outputPath}
+ ln -sf ~{select_first(gvcfFileIndexes)} ~{outputPath}.tbi
fi
}
@@ -156,13 +162,15 @@ task CombineGVCFs {
# Combine multiple recalibration tables from scattered BaseRecalibrator runs
task GatherBqsrReports {
- String? preCommand
- String? gatkJar
- Array[File] inputBQSRreports
- String outputReportPath
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ String? gatkJar
+ Array[File] inputBQSRreports
+ String outputReportPath
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -172,11 +180,11 @@ task GatherBqsrReports {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
GatherBQSRReports \
- -I ${sep=' -I ' inputBQSRreports} \
- -O ${outputReportPath}
+ -I ~{sep=' -I ' inputBQSRreports} \
+ -O ~{outputReportPath}
}
output {
@@ -189,25 +197,27 @@ task GatherBqsrReports {
}
task GenotypeGVCFs {
- String? preCommand
- File gvcfFiles
- File gvcfFileIndexes
- Array[File]+ intervals
+ input {
+ String? preCommand
+ File gvcfFiles
+ File gvcfFileIndexes
+ Array[File]+ intervals
- String outputPath
+ String outputPath
- String? gatkJar
+ String? gatkJar
- File refFasta
- File refFastaIndex
- File refDict
+ File refFasta
+ File refFastaIndex
+ File refDict
- File? dbsnpVCF
- File? dbsnpVCFindex
+ File? dbsnpVCF
+ File? dbsnpVCFindex
- Int? compressionLevel
- Float? memory
- Float? memoryMultiplier
+ Int? compressionLevel
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
@@ -217,18 +227,18 @@ task GenotypeGVCFs {
command {
set -e -o pipefail
- ${preCommand}
+ ~{preCommand}
- ${toolCommand} \
+ ~{toolCommand} \
GenotypeGVCFs \
- -R ${refFasta} \
- -O ${outputPath} \
- ${"-D " + dbsnpVCF} \
+ -R ~{refFasta} \
+ -O ~{outputPath} \
+ ~{"-D " + dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
- -V ${gvcfFiles} \
- -L ${sep=' -L ' intervals}
+ -V ~{gvcfFiles} \
+ -L ~{sep=' -L ' intervals}
}
output {
@@ -243,23 +253,25 @@ task GenotypeGVCFs {
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
task HaplotypeCallerGvcf {
- String? preCommand
- Array[File]+ inputBams
- Array[File]+ inputBamsIndex
- Array[File]+ intervalList
- String gvcfPath
- File refDict
- File refFasta
- File refFastaIndex
- Float? contamination
- Int? compressionLevel
- String? gatkJar
-
- File? dbsnpVCF
- File? dbsnpVCFindex
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
+ Array[File]+ intervalList
+ String gvcfPath
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Float? contamination
+ Int? compressionLevel
+ String? gatkJar
+
+ File? dbsnpVCF
+ File? dbsnpVCFindex
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
@@ -268,15 +280,15 @@ task HaplotypeCallerGvcf {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
HaplotypeCaller \
- -R ${refFasta} \
- -O ${gvcfPath} \
- -I ${sep=" -I " inputBams} \
- -L ${sep=' -L ' intervalList} \
- ${"-D " + dbsnpVCF} \
- -contamination ${default=0 contamination} \
+ -R ~{refFasta} \
+ -O ~{gvcfPath} \
+ -I ~{sep=" -I " inputBams} \
+ -L ~{sep=' -L ' intervalList} \
+ ~{"-D " + dbsnpVCF} \
+ -contamination ~{default=0 contamination} \
-ERC GVCF
}
@@ -291,19 +303,21 @@ task HaplotypeCallerGvcf {
}
task SplitNCigarReads {
- String? preCommand
-
- File inputBam
- File inputBamIndex
- File refFasta
- File refFastaIndex
- File refDict
- String outputBam
- String? gatkJar
- Array[File]+ intervals
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+
+ File inputBam
+ File inputBamIndex
+ File refFasta
+ File refFastaIndex
+ File refDict
+ String outputBam
+ String? gatkJar
+ Array[File]+ intervals
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
@@ -312,13 +326,13 @@ task SplitNCigarReads {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
+ ~{preCommand}
+ ~{toolCommand} \
SplitNCigarReads \
- -I ${inputBam} \
- -R ${refFasta} \
- -O ${outputBam} \
- -L ${sep=' -L ' intervals}
+ -I ~{inputBam} \
+ -R ~{refFasta} \
+ -O ~{outputBam} \
+ -L ~{sep=' -L ' intervals}
}
output {
--
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