Merge branch 'fix-flexiprep' into 'develop'

Fix flexiprep

Fixing some small issue here found in integration tests.

See merge request !247

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

@@ -53,6 +53,8 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
   @Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
   var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
 
+  override def defaultCoreMemory = 8.0
+
   override def beforeGraph() {
     super.beforeGraph()
     if (outputChart == null) outputChart = new File(output + ".pdf")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala

@@ -33,7 +33,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
 
   javaMainClass = new picard.analysis.CollectMultipleMetrics().getClass.getName
 
-  override def defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 8.0
 
   @Input(doc = "The input SAM or BAM files to analyze", required = true)
   var input: File = null

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

@@ -201,7 +201,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
 
   def summaryStats: Map[String, Any] = Map(
     "per_base_sequence_quality" -> perBaseSequenceQuality,
-    "per_base_sequence_content" -> perBaseSequenceContent)
+    "per_base_sequence_content" -> perBaseSequenceContent,
+    "adapters" -> foundAdapters.map(x => x.name -> x.seq).toMap)
 }
 
 object Fastqc {

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

@@ -250,24 +250,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     if (fastq_R1.length != fastq_R2.length && paired)
       throw new IllegalStateException("R1 and R2 file number is not the same")
 
-    if (!skipTrim || !skipClip) {
-      if (fastq_R1.length > 1) {
-        add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
-        if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
-      }
+    if (fastq_R1.length > 1) {
+      add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
+      if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
+    }
 
-      outputFiles += ("output_R1_gzip" -> fastqR1Qc)
-      if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
+    outputFiles += ("output_R1_gzip" -> fastqR1Qc)
+    if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
 
-      fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
-      add(fastqc_R1_after)
-      addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
+    fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
+    add(fastqc_R1_after)
+    addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
 
-      if (paired) {
-        fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
-        add(fastqc_R2_after)
-        addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
-      }
+    if (paired) {
+      fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
+      add(fastqc_R2_after)
+      addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
     }
 
     addSummaryJobs()

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -73,11 +73,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     flexiprep.libId = Some("1")
     flexiprep.script()
 
-    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (
-      if (paired && (skipClip && skipTrim)) 2
-      else if (!paired && (skipClip && skipTrim)) 1
-      else if (paired && !(skipClip && skipTrim)) 4
-      else if (!paired && !(skipClip && skipTrim)) 2)
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (paired) 4 else 2)
     flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
   }