gatk to 1.0

0e6bde49 · Ruben Vorderman · 9249f3e2 · 0e6bde49
Commit 0e6bde49 authored 6 years ago by Ruben Vorderman
--- a/gatk.wdl
+++ b/gatk.wdl
+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 {