Merge pull request #57 from biowdl/BIOWDL-88

Fixed defaults

bwa.wdl

@@ -39,12 +39,14 @@ task Mem {
     String picardCommand = if (defined(bwaIndex.altIndex)) then sortSamCommand + " | " + setNmMdAndUqTagsCommand
     else sortSamCommand
 
+    String readgroupArg = if (defined(readgroup)) then "-R '" + readgroup + "'" else ""
+
     command {
         set -e -o pipefail
         mkdir -p $(dirname ~{outputPath})
         ~{preCommand}
         bwa mem ~{"-t " + threads} \
-        ~{"-R '" + readgroup + "'"} \
+        ~{readgroupArg} \
         ~{bwaIndex.fastaFile} \
         ~{inputR1} \
         ~{inputR2} \
@@ -53,9 +55,9 @@ task Mem {
     }
 
     output {
-        IndexedBamFile bamFile = {
-          "file": outputPath,
-          "index": sub(outputPath, ".bam$", ".bai")
+        IndexedBamFile bamFile = object {
+          file: outputPath,
+          index: sub(outputPath, ".bam$", ".bai")
         }
     }
 
@@ -92,9 +94,9 @@ task Index {
     }
 
     output {
-        BwaIndex outputIndex = {
-            "fastaFile": outputFile,
-            "indexFiles": [outputFile + ".bwt",outputFile + ".pac",outputFile + ".sa",outputFile + ".amb",outputFile + ".ann"]
+        BwaIndex outputIndex = object {
+            fastaFile: outputFile,
+            indexFiles: [outputFile + ".bwt",outputFile + ".pac",outputFile + ".sa",outputFile + ".amb",outputFile + ".ann"]
         }
     }
 

seqtk.wdl

@@ -6,7 +6,7 @@ task Sample {
         String outFilePath = "subsampledReads.fq.gz"
         String? preCommand
         Int? seed
-        Boolean twoPassMode
+        Boolean twoPassMode = false
         Float? fraction
         Int? number
         Boolean zip = true

spades.wdl

@@ -32,7 +32,8 @@ task Spades {
         Int? phredOffset
     }
 
-    Int clusterMemory = ceil(memoryGb / threads)
+    Int clusterMemory = ceil(memoryGb / threads * 1.2)
+    Int memoryArg = ceil(memoryGb)
 
     command {
         set -e -o pipefail
@@ -60,7 +61,7 @@ task Spades {
         ~{true="--disable-rr" false="" disableRepeatResolution} \
         ~{"--dataset " + dataset} \
         ~{"--threads " + threads} \
-        ~{"--memory " + memoryGb} \
+        ~{"--memory " + memoryArg} \
         ~{"-k " + k} \
         ~{"--cov-cutoff " + covCutoff} \
         ~{"--phred-offset " + phredOffset}