Merge remote-tracking branch 'origin/develop' into controlTreat

biopet/sampleconfig.wdl

 version 1.0
 
+import "../common.wdl" as common
+
 task SampleConfig {
     input {
         File? toolJar
@@ -77,3 +79,41 @@ task SampleConfigCromwellArrays {
         memory: ceil(memory * memoryMultiplier)
     }
 }
+
+task CaseControl {
+    input {
+        File? toolJar
+        String? preCommand
+        Array[File]+ inputFiles
+        Array[File]+ sampleConfigs
+        String outputPath
+        String controlTag = "control"
+
+        Int memory = 4
+        Float memoryMultiplier = 1.5
+    }
+
+    String toolCommand = if defined(toolJar)
+        then "java -Xmx" + memory + "G -jar " + toolJar
+        else "biopet-sampleconfig -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p $(dirname ~{outputPath})
+        ~{toolCommand} CromwellArrays \
+        -i ~{sep="-i " inputFiles} \
+        -s ~{sep="-s " sampleConfigs} \
+        ~{"-o " + outputPath} \
+        ~{"--controlTag " + controlTag}
+    }
+
+    output {
+        File outputFile = outputPath
+        Array[CaseControl] caseControls = read_json(outputFile)
+    }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
+}

common.wdl

@@ -163,3 +163,10 @@ struct FastqPair {
     File? R2
     File? R2_md5
 }
+
+struct CaseControl {
+    String inputName
+    IndexedBamFile inputBam
+    String controlName
+    IndexedBamFile controlBam
+}

gatk.wdl

@@ -123,18 +123,12 @@ task CombineGVCFs {
     command {
         set -e -o pipefail
         ~{preCommand}
-
-        if [ ~{length(gvcfFiles)} -gt 1 ]; then
-            ~{toolCommand} \
-             CombineGVCFs \
-             -R ~{reference.fasta} \
-             -O ~{outputPath} \
-             -V ~{sep=' -V ' gvcfFiles} \
-             -L ~{sep=' -L ' intervals}
-        else # TODO this should be handeled in wdl
-            ln -sf ~{gvcfFiles[0]} ~{outputPath}
-            ln -sf ~{gvcfFiles[0]} ~{outputPath}.tbi
-        fi
+        ~{toolCommand} \
+        CombineGVCFs \
+        -R ~{reference.fasta} \
+        -O ~{outputPath} \
+        -V ~{sep=' -V ' gvcfFiles} \
+        -L ~{sep=' -L ' intervals}
     }
 
     output {