Merge branch 'fix-make-rc_trimmingoptional' into 'develop'

enableRCtrimming is used to enable trimming of Reverse Complement versions of adapters

Make trimming of Reverse complement version of adapters optional (by default enableRCtrimming=false)

See merge request !393

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

@@ -35,6 +35,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
 
   /** Allow reporting of all found (potentially adapter) sequences in the FastQC */
   var sensitiveAdapterSearch: Boolean = config("sensitiveAdapterSearch", default = false)
+  var enableRCtrimming: Boolean = config("enableRCtrimming", default = false)
 
   /** Class for storing a single FastQC module result */
   protected case class FastQCModule(name: String, status: String, lines: Seq[String])
@@ -188,9 +189,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
       val fromKnownList: Set[AdapterSequence] = (adapterSet ++ contaminantSet)
         .filter(x => foundAdapterNames.exists(_.startsWith(x.name)))
 
-      val fromKnownListRC: Set[AdapterSequence] = fromKnownList.map {
+      val fromKnownListRC: Set[AdapterSequence] = if (enableRCtrimming) fromKnownList.map {
         x => AdapterSequence(x.name + "_RC", reverseComplement(x.seq))
       }
+      else Set.empty
 
       // list all sequences found by FastQC
       val fastQCFoundSequences: Seq[AdapterSequence] = if (sensitiveAdapterSearch) {

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala

@@ -27,7 +27,7 @@ class CutadaptTest extends FastqcV0101Test {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.contaminants = Option(resourceFile("fqc_contaminants_v0112.txt"))
-    //    fqc.beforeGraph()
+    fqc.enableRCtrimming = true
     fqc
   }
 

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala

@@ -73,11 +73,15 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     fqc.contaminants = Option(resourceFile("fqc_contaminants_v0101.txt"))
     // found adapters also contain the adapters in reverse complement (done within flexiprep/fastqc only)
     val adapters = fqc.foundAdapters
-    // we find 1 adapter which comes with the Reverse Complement counterpart
-    adapters.size shouldBe 2
 
-    adapters.head.name shouldEqual "TruSeq Adapter, Index 1_RC"
-    adapters.head.seq shouldEqual "CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
+    if (fqc.enableRCtrimming) {
+      // we find 1 adapter which comes with the Reverse Complement counterpart
+      adapters.size shouldBe 2
+      adapters.head.name shouldEqual "TruSeq Adapter, Index 1_RC"
+      adapters.head.seq shouldEqual "CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
+    } else {
+      adapters.size shouldBe 1
+    }
 
     adapters.last.name shouldEqual "TruSeq Adapter, Index 1"
     adapters.last.seq shouldEqual "GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"