Dockerize GATK. Scattering now works with containers. Tabix another docker image.

gatk.wdl

@@ -5,8 +5,6 @@ import "common.wdl"
 # Apply Base Quality Score Recalibration (BQSR) model
 task ApplyBQSR {
     input {
-        String? preCommand
-        File? gatkJar
         IndexedBamFile inputBam
         String outputBamPath
         File recalibrationReport
@@ -18,26 +16,21 @@ task ApplyBQSR {
         String dockerTag = "4.1.0.0--0"
     }
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
-         ApplyBQSR \
-         --create-output-bam-md5 \
-         --add-output-sam-program-record \
-         -R ~{reference.fasta} \
-         -I ~{inputBam.file} \
-         --use-original-qualities \
-         -O ~{outputBamPath} \
-         -bqsr ~{recalibrationReport} \
-         --static-quantized-quals 10 \
-         --static-quantized-quals 20 \
-         --static-quantized-quals 30 \
-         -L ~{sep=" -L " sequenceGroupInterval}
+        gatk --java-options -Xmx~{memory}G \
+        ApplyBQSR \
+        --create-output-bam-md5 \
+        --add-output-sam-program-record \
+        -R ~{reference.fasta} \
+        -I ~{inputBam.file} \
+        --use-original-qualities \
+        -O ~{outputBamPath} \
+        -bqsr ~{recalibrationReport} \
+        --static-quantized-quals 10 \
+        --static-quantized-quals 20 \
+        --static-quantized-quals 30 \
+        -L ~{sep=" -L " sequenceGroupInterval}
     }
 
     output {
@@ -57,8 +50,6 @@ task ApplyBQSR {
 # Generate Base Quality Score Recalibration (BQSR) model
 task BaseRecalibrator {
     input {
-        String? preCommand
-        File? gatkJar
         IndexedBamFile inputBam
         String recalibrationReportPath
         Array[File]+ sequenceGroupInterval
@@ -76,14 +67,9 @@ task BaseRecalibrator {
         [select_first([dbsnpVCF]).file]
     ])
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         BaseRecalibrator \
         -R ~{reference.fasta} \
         -I ~{inputBam.file} \
@@ -105,14 +91,12 @@ task BaseRecalibrator {
 
 task CombineGVCFs {
     input {
-        String? preCommand
         Array[File]+ gvcfFiles
         Array[File]+ gvcfFilesIndex
         Array[File]+ intervals
 
         String outputPath
 
-        String? gatkJar
 
         Reference reference
 
@@ -121,14 +105,9 @@ task CombineGVCFs {
         String dockerTag = "4.1.0.0--0"
     }
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         CombineGVCFs \
         -R ~{reference.fasta} \
         -O ~{outputPath} \
@@ -152,8 +131,6 @@ task CombineGVCFs {
 # Combine multiple recalibration tables from scattered BaseRecalibrator runs
 task GatherBqsrReports {
     input {
-        String? preCommand
-        String? gatkJar
         Array[File] inputBQSRreports
         String outputReportPath
 
@@ -162,14 +139,9 @@ task GatherBqsrReports {
         String dockerTag = "4.1.0.0--0"
     }
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         GatherBQSRReports \
         -I ~{sep=' -I ' inputBQSRreports} \
         -O ~{outputReportPath}
@@ -187,15 +159,12 @@ task GatherBqsrReports {
 
 task GenotypeGVCFs {
     input {
-        String? preCommand
         Array[File]+ gvcfFiles
         Array[File]+ gvcfFilesIndex
         Array[File]+ intervals
 
         String outputPath
 
-        String? gatkJar
-
         Reference reference
 
         IndexedVcfFile? dbsnpVCF
@@ -207,14 +176,9 @@ task GenotypeGVCFs {
 
     File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         GenotypeGVCFs \
         -R ~{reference.fasta} \
         -O ~{outputPath} \
@@ -242,14 +206,12 @@ task GenotypeGVCFs {
 # Call variants on a single sample with HaplotypeCaller to produce a GVCF
 task HaplotypeCallerGvcf {
     input {
-        String? preCommand
         Array[File]+ inputBams
         Array[File]+ inputBamsIndex
         Array[File]+ intervalList
         String gvcfPath
         Reference reference
         Float contamination = 0.0
-        String? gatkJar
 
         IndexedVcfFile? dbsnpVCF
 
@@ -260,15 +222,11 @@ task HaplotypeCallerGvcf {
 
     File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
         mkdir -p $(dirname ~{gvcfPath})
-        ~{preCommand}
-        gatk --java-options -Xmx~{memory}G HaplotypeCaller \
+        gatk --java-options -Xmx~{memory}G \
+        HaplotypeCaller \
         -R ~{reference.fasta} \
         -O ~{gvcfPath} \
         -I ~{sep=" -I " inputBams} \
@@ -293,8 +251,6 @@ task HaplotypeCallerGvcf {
 
 task MuTect2 {
     input {
-        String? preCommand
-
         Array[File]+ inputBams
         Array[File]+ inputBamsIndex
         Reference reference
@@ -303,20 +259,14 @@ task MuTect2 {
         String? normalSample
         Array[File]+ intervals
 
-        String? gatkJar
         Int memory = 4
         Float memoryMultiplier = 3
         String dockerTag = "4.1.0.0--0"
     }
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         Mutect2 \
         -R ~{reference.fasta} \
         -I ~{sep=" -I " inputBams} \
@@ -341,12 +291,9 @@ task MuTect2 {
 
 task SplitNCigarReads {
     input {
-        String? preCommand
-
         IndexedBamFile inputBam
         Reference reference
         String outputBam
-        String? gatkJar
         Array[File]+ intervals
 
         Int memory = 4
@@ -354,14 +301,9 @@ task SplitNCigarReads {
         String dockerTag = "4.1.0.0--0"
     }
 
-    String toolCommand = if defined(gatkJar)
-        then "java -Xmx" + memory + "G -jar " + gatkJar
-        else "gatk --java-options -Xmx" + memory + "G"
-
     command {
         set -e -o pipefail
-        ~{preCommand}
-        ~{toolCommand} \
+        gatk --java-options -Xmx~{memory}G \
         SplitNCigarReads \
         -I ~{inputBam.file} \
         -R ~{reference.fasta} \