Merge branch 'BIOWDL-120' of https://github.com/biowdl/tasks into BIOWDL-120

biopet/bamstats.wdl

@@ -15,7 +15,7 @@ task Generate {
         Boolean tsvOutputs = false
         String outputDir
         Reference? reference
-        Int memory = 4
+        Int memory = 8
         Float memoryMultiplier = 2.0
     }
 

biopet/biopet.wdl

@@ -236,6 +236,7 @@ task ScatterRegions {
         File? toolJar
         Int? scatterSize
         File? regions
+        Boolean notSplitContigs = false
 
         Int memory = 4
         Float memoryMultiplier = 3.0
@@ -253,7 +254,8 @@ task ScatterRegions {
           -R ~{reference.fasta} \
           -o ~{outputDirPath} \
           ~{"-s " + scatterSize} \
-          ~{"-L " + regions}
+          ~{"-L " + regions} \
+          ~{true="--notSplitContigs" false="" notSplitContigs}
     }
 
     output {

fastqc.wdl

@@ -21,10 +21,10 @@ task Fastqc {
     }
 
     # Chops of the .gz extension if present.
-    String name = sub(seqFile, "\.gz$","")
+    String name = basename(sub(seqFile, "\.gz$","")) # The Basename needs to be taken here. Otherwise paths might differ between similar jobs.
     # This regex chops of the extension and replaces it with _fastqc for the reportdir.
     # Just as fastqc does it.
-    String reportDir = outdirPath + "/" + sub(basename(name), "\.[^\.]*$", "_fastqc")
+    String reportDir = outdirPath + "/" + sub(name, "\.[^\.]*$", "_fastqc")
 
     command {
         set -e -o pipefail