diff --git a/gatk.wdl b/gatk.wdl
index 37d60355bc36e284ab2a00c0ba8bbfe24abe9022..dbe4e0c7f29d83e56f117e45c4a2100e6158955a 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1,16 +1,15 @@
-# Generate Base Quality Score Recalibration (BQSR) model
-task BaseRecalibrator {
+# Apply Base Quality Score Recalibration (BQSR) model
+task ApplyBQSR {
String? preCommand
- String gatk_jar
- String input_bam
- String input_bam_index
- String recalibration_report_filename
- Array[File]+ sequence_group_interval
- Array[File]+ known_indels_sites_VCFs
- Array[File]+ known_indels_sites_indices
- File ref_dict
- File ref_fasta
- File ref_fasta_index
+ File gatkJar
+ File inputBam
+ String outputBamPath
+ File recalibrationReport
+ Array[File]+ sequenceGroupInterval
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -19,18 +18,23 @@ task BaseRecalibrator {
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatk_jar} \
- BaseRecalibrator \
- -R ${ref_fasta} \
- -I ${input_bam} \
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xms${mem}G -jar ${gatkJar} \
+ ApplyBQSR \
+ --create-output-bam-md5 \
+ --add-output-sam-program-record \
+ -R ${refFasta} \
+ -I ${inputBam} \
--use-original-qualities \
- -O ${recalibration_report_filename} \
- --known-sites ${sep=" --known-sites " known_indels_sites_VCFs} \
- -L ${sep=" -L " sequence_group_interval}
+ -O ${outputBamPath} \
+ -bqsr ${recalibrationReport} \
+ --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
+ -L ${sep=" -L " sequenceGroupInterval}
}
output {
- File recalibration_report = "${recalibration_report_filename}"
+ File recalibrated_bam = outputBamPath
+ File recalibrated_bam_checksum = outputBamPath + ".md5"
}
runtime {
@@ -38,18 +42,19 @@ task BaseRecalibrator {
}
}
-# Apply Base Quality Score Recalibration (BQSR) model
-task ApplyBQSR {
+# Generate Base Quality Score Recalibration (BQSR) model
+task BaseRecalibrator {
String? preCommand
- String gatk_jar
- String input_bam
- String output_bam_path
- File recalibration_report
- Array[String] sequence_group_interval
- File ref_dict
- File ref_fasta
- File ref_fasta_index
- Int? compression_level
+ File gatkJar
+ File inputBam
+ File inputBamIndex
+ String recalibrationReportPath
+ Array[File]+ sequenceGroupInterval
+ Array[File]+ knownIndelsSitesVCFs
+ Array[File]+ knownIndelsSitesIndices
+ File refDict
+ File refFasta
+ File refFastaIndex
Float? memory
Float? memoryMultiplier
@@ -58,23 +63,18 @@ task ApplyBQSR {
command {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xms${mem}G -jar ${gatk_jar} \
- ApplyBQSR \
- --create-output-bam-md5 \
- --add-output-sam-program-record \
- -R ${ref_fasta} \
- -I ${input_bam} \
+ java -Xms${mem}G -jar ${gatkJar} \
+ BaseRecalibrator \
+ -R ${refFasta} \
+ -I ${inputBam} \
--use-original-qualities \
- -O ${output_bam_path} \
- -bqsr ${recalibration_report} \
- --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
- -L ${sep=" -L " sequence_group_interval}
+ -O ${recalibrationReportPath} \
+ --known-sites ${sep=" --known-sites " knownIndelsSitesVCFs} \
+ -L ${sep=" -L " sequenceGroupInterval}
}
output {
- File recalibrated_bam = "${output_bam_path}"
- File recalibrated_bam_checksum = "${output_bam_path}.md5"
+ File recalibrationReport = recalibrationReportPath
}
runtime {
@@ -82,13 +82,21 @@ task ApplyBQSR {
}
}
-# Combine multiple recalibration tables from scattered BaseRecalibrator runs
-task GatherBqsrReports {
+task CombineGVCFs {
String? preCommand
- String gatk_jar
- Array[File] input_bqsr_reports
- String output_report_filepath
+ Array[File]+ gvcfFiles
+ Array[File]+ gvcfFileIndexes
+ Array[File]+ intervals
+ String outputPath
+
+ String gatkJar
+
+ File refFasta
+ File refFastaIndex
+ File refDict
+
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -96,14 +104,24 @@ task GatherBqsrReports {
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatk_jar} \
- GatherBQSRReports \
- -I ${sep=' -I ' input_bqsr_reports} \
- -O ${output_report_filepath}
+
+ if [ ${length(gvcfFiles)} -gt 1 ]; then
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
+ CombineGVCFs \
+ -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)} ${outputPath}.tbi
+ fi
}
output {
- File output_bqsr_report = "${output_report_filepath}"
+ File outputGVCF = outputPath
+ File outputGVCFindex = outputPath + ".tbi"
}
runtime {
@@ -111,19 +129,12 @@ task GatherBqsrReports {
}
}
-# Call variants on a single sample with HaplotypeCaller to produce a GVCF
-task HaplotypeCallerGvcf {
+# Combine multiple recalibration tables from scattered BaseRecalibrator runs
+task GatherBqsrReports {
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
+ Array[File] inputBQSRreports
+ String outputReportPath
Float? memory
Float? memoryMultiplier
@@ -132,20 +143,14 @@ task HaplotypeCallerGvcf {
command {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compressionLevel} \
- -Xmx${mem}G -jar ${gatkJar} \
- HaplotypeCaller \
- -R ${refFasta} \
- -O ${gvcfPath} \
- -I ${sep=" -I " inputBams} \
- -L ${sep=' -L ' intervalList} \
- -contamination ${default=0 contamination} \
- -ERC GVCF
+ java -Xms${mem}G -jar ${gatkJar} \
+ GatherBQSRReports \
+ -I ${sep=' -I ' inputBQSRreports} \
+ -O ${outputReportPath}
}
output {
- File outputGVCF = gvcfPath
- File outputGVCFindex = gvcfPath + ".tbi"
+ File outputBQSRreport = outputReportPath
}
runtime {
@@ -202,21 +207,20 @@ task GenotypeGVCFs {
}
}
-task CombineGVCFs {
+# Call variants on a single sample with HaplotypeCaller to produce a GVCF
+task HaplotypeCallerGvcf {
String? preCommand
- Array[File]+ gvcfFiles
- Array[File]+ gvcfFileIndexes
- Array[File]+ intervals
-
- String outputPath
-
- String gatkJar
-
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
+ Array[File]+ intervalList
+ String gvcfPath
+ File refDict
File refFasta
File refFastaIndex
- File refDict
-
+ Float? contamination
Int? compressionLevel
+ String gatkJar
+
Float? memory
Float? memoryMultiplier
@@ -224,24 +228,20 @@ task CombineGVCFs {
command {
set -e -o pipefail
${preCommand}
-
- if [ ${length(gvcfFiles)} -gt 1 ]; then
- java ${"-Dsamjdk.compression_level=" + compressionLevel} \
- -Xmx${mem}G -jar ${gatkJar} \
- CombineGVCFs \
- -R ${refFasta} \
- -O ${outputPath} \
- -V ${sep=' -V ' gvcfFiles} \
- -L ${sep=' -L ' intervals}
- else
- ln -sf ${select_first(gvcfFiles)} ${outputPath}
- ln -sf ${select_first(gvcfFileIndexes)} ${outputPath}.tbi
- fi
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
+ HaplotypeCaller \
+ -R ${refFasta} \
+ -O ${gvcfPath} \
+ -I ${sep=" -I " inputBams} \
+ -L ${sep=' -L ' intervalList} \
+ -contamination ${default=0 contamination} \
+ -ERC GVCF
}
output {
- File outputGVCF = outputPath
- File outputGVCFindex = outputPath + ".tbi"
+ File outputGVCF = gvcfPath
+ File outputGVCFindex = gvcfPath + ".tbi"
}
runtime {