Fixed output files of fastqc

fastqc.wdl

@@ -40,14 +40,9 @@ task fastqc {
     }
 
     output {
-        # Chops of the .gz extension if present.
-        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")
-        File rawReport = reportDir + "/fastqc_data.txt"
-        File htmlReport = reportDir + "/fastqc_report.html"
-        File summary = reportDir + "/summary.txt"
+        File rawReport = outdirPath + "/*/fastqc_data.txt"
+        File htmlReport = outdirPath + "/*/fastqc_report.html"
+        File summary = outdirPath + "/*/summary.txt"
         Array[File] images = glob(outdirPath + "/*/Images/*.png")
     }