Merge branch 'feature-autodetect_paired' into 'develop'

Added autodetect fileformat paired

Fixed #350 

See merge request !414

carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config._
 import org.broadinstitute.gatk.queue.QScript
 
@@ -49,7 +50,8 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
     "samtoolsview" -> Map(
       "h" -> true,
       "b" -> true
-    )
+    ),
+    "macs2callpeak" -> Map("fileformat" -> "")
   )
 
   def summaryFile = new File(outputDir, "Carp.summary.json")
@@ -91,6 +93,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
       macs2.treatment = preProcessBam.get
       macs2.name = Some(sampleId)
       macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
+      macs2.fileformat = if (paired) Some("BAMPE") else Some("BAM")
       add(macs2)
     }
   }
@@ -102,6 +105,13 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
     Some(carp)
   }
 
+  lazy val paired: Boolean = {
+    val notPaired = samples.forall(_._2.libraries.forall(_._2.inputR2.isEmpty))
+    val p = samples.forall(_._2.libraries.forall(_._2.inputR2.isDefined))
+    if (!notPaired && !p) Logging.addError("Combination of Paired-end and Single-end detected, this is not allowed in Carp")
+    p
+  }
+
   override def init() = {
     super.init()
     // ensure that no samples are called 'control' since that is our reserved keyword
@@ -119,6 +129,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
         macs2.treatment = sample.preProcessBam.get
         macs2.control = samples(controlId).preProcessBam.get
         macs2.name = Some(sampleId + "_VS_" + controlId)
+        macs2.fileformat = if (paired) Some("BAMPE") else Some("BAM")
         macs2.outputdir = sample.sampleDir + File.separator + "macs2" + File.separator + macs2.name.get + File.separator
         add(macs2)
       }