diff --git a/.gitignore b/.gitignore
index 916e17c097a497c47e0e200e5b4acd5c3f4f42ac..48aaec461ce9756ebd2a35fda38286b09bd9c5f8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
 dependency-reduced-pom.xml
+*~
+*.swp
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index d0ce249e06e65517f3b58c1cccbfb1f47c9cadee..53a72bf17262e4c351ad2391773f031db629e23e 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -92,4 +92,4 @@ object Fastqc {
     fastqcCommand.afterGraph
     return fastqcCommand
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index ecc911a7720341d2a8e9d4957adceb0875f72238..f2fc812ee2b75ebddf37a328196480f7373f1d11 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -82,12 +82,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     if (paired) addSha1sum(outputFiles("fastq_input_R2"), "sha1_R2")
 
     var fastqc_R1 = Fastqc(this, input_R1, outputDir + "/" + R1_name + ".fastqc/")
+    add(fastqc_R1)
     outputFiles += ("fastqc_R1" -> fastqc_R1.output)
     outputFiles += ("qualtype_R1" -> getQualtype(fastqc_R1, R1_name))
     outputFiles += ("contams_R1" -> getContams(fastqc_R1, R1_name))
 
     if (paired) {
       var fastqc_R2 = Fastqc(this, input_R2, outputDir + "/" + R2_name + ".fastqc/")
+      add(fastqc_R2)
       outputFiles += ("fastqc_R2" -> fastqc_R2.output)
       outputFiles += ("qualtype_R2" -> getQualtype(fastqc_R2, R2_name))
       outputFiles += ("contams_R2" -> getContams(fastqc_R2, R2_name))
@@ -232,9 +234,14 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
 
       addSha1sum(R1, "sha1_qc_R1")
       if (paired) addSha1sum(R2, "sha1_qc_R2")
-      
-      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)
+      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)
+      }
     }
 
     if (!skipSummary) {