Merge branch 'patch-carp' into 'develop'

Patch carp

Merge to fix the wrong directory of MACS2 single samples runs

See merge request !113

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

@@ -44,7 +44,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
 
   var pairs: Boolean = config("pairs", default = false)
 
-  override val defaultVmem = "4G"
+  override val defaultVmem = "6G"
 
   override def beforeGraph {
     super.beforeGraph

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

@@ -81,7 +81,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
       conditional(verbose, "--verbose") + /* Whether to output verbosely */
       optional("--tsize", tsize) + /* Sets custom tag length, if not specified macs will use first 10 sequences to estimate the size */
       optional("--bw", bandwith) + /* The bandwith to use for model building. Set this parameter as the sonication fragment size estimated in the wetlab */
-      optional("'--mfold'", repeat(mfold), escape = false) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
+      (if (mfold.isEmpty) "" else optional("'--mfold'", repeat(mfold), escape = false)) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
       conditional(fixbimodel, "--fix-bimodal") + /* Whether turn on the auto paired-peak model process. If it's set, when MACS failed to build paired model, it will use the nomodel settings, the '--extsize' parameter to extend each tags. If set, MACS will be terminated if paried-peak model is failed. */
       conditional(nomodel, "--nomodel") + /* While on, MACS will bypass building the shifting model */
       optional("--shift", shift) + /* You can set an arbitrary shift in basepairs here */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala

@@ -38,8 +38,8 @@ class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction with
   @Output(doc = "Output JSON", shortName = "output", required = true)
   var output: File = null
 
-  override val defaultVmem = "4G"
-  memoryLimit = Option(3.0)
+  override val defaultVmem = "3G"
+  memoryLimit = Option(1.0)
 
   override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
 

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

@@ -110,7 +110,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
       val macs2 = new Macs2CallPeak(qscript)
       macs2.treatment = bamFile
       macs2.name = Some(sampleId)
-      macs2.outputdir = sampleDir + "macs2/" + sampleId + "/"
+      macs2.outputdir = sampleDir + File.separator + "macs2" + File.separator + sampleId + File.separator
       add(macs2)
     }
   }
@@ -137,7 +137,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
         macs2.treatment = sample.bamFile
         macs2.control = samples(controlId).bamFile
         macs2.name = Some(sampleId + "_VS_" + controlId)
-        macs2.outputdir = sample.sampleDir + "/" + "macs2/" + macs2.name.get + "/"
+        macs2.outputdir = sample.sampleDir + File.separator + "macs2" + File.separator + macs2.name.get + File.separator
         add(macs2)
       }
     }