Revert "Fix on fastqc jobs"

This reverts commit 5945ab1746a433f4c9c2100176934d7ee86c38a2.

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

@@ -62,7 +62,7 @@ object Fastqc {
     if (filename.endsWith(".gzip")) filename = filename.substring(0, filename.size - 5)
     if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.size - 6)
     //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
-    fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
+    fastqcCommand.jobOutputFile = new File(outDir + "/" + filename + "_fastqc.zip")
     fastqcCommand.afterGraph
     return fastqcCommand
   }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -81,18 +81,16 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     addSha1sum(outputFiles("fastq_input_R1"), "sha1_R1")
     if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
 
-    val fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
+    var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
     outputFiles += ("fastqc_R1" -> fastqc_R1.output)
     outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
     outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
-    add(fastqc_R1)
-    
+
     if (paired) {
-      val fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
+      var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
       outputFiles += ("fastqc_R2" -> fastqc_R2.output)
       outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
       outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
-      add(fastqc_R2)
     }
   }
 
@@ -235,14 +233,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
       addSha1sum(R1, "sha1_qc_R1")
       if (paired) addSha1sum(R2, "sha1_qc_R2")
       
-      val fastqc_R1 = Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/")
-      add(fastqc_R1)
-      outputFiles += ("fastqc_R1_final" -> fastqc_R1.output)
-      if (paired) {
-        val fastqc_R2 = Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/")
-        add(fastqc_R2)
-        outputFiles += ("fastqc_R2_final" -> fastqc_R2.output)
-      }
+      outputFiles += ("fastqc_R1_final" -> Fastqc(this, outputFiles("output_R1"), outputDir + "/" + R1_name + ".qc.fastqc/").output)
+      if (paired) outputFiles += ("fastqc_R2_final" -> Fastqc(this, outputFiles("output_R2"), outputDir + "/" + R2_name + ".qc.fastqc/").output)
     }
 
     if (!skipSummary) {