Merge pull request #47 from biowdl/BIOWDL-68

Fix fastqc and cutadapt for use with WDL 1.0

cutadapt.wdl

@@ -61,10 +61,12 @@ task Cutadapt {
         String? reportPath
     }
 
+    String read2outputArg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else ""
+
     command {
         set -e -o pipefail
         ~{"mkdir -p $(dirname " + read1output + ")"}
-        ~{"mkdir -p $(dirname " + read2output + ")"}
+        ~{read2outputArg}
         ~{"mkdir -p $(dirname " + reportPath + ")"}
         ~{preCommand}
         cutadapt \

fastqc.wdl

@@ -21,10 +21,10 @@ task Fastqc {
     }
 
     # Chops of the .gz extension if present.
-    String name = sub(seqFile, "\\.gz$","")
+    String name = sub(seqFile, "\.gz$","")
     # 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), "\\.[^\\.]*$", "_fastqc")
+    String reportDir = outdirPath + "/" + sub(basename(name), "\.[^\.]*$", "_fastqc")
 
     command {
         set -e -o pipefail