Merge branch 'feature-igvtools' into 'develop'

Fix igvtools

This starts igvtools directly from the jar instead using the wrapper from igvtools itself

See merge request !448

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

@@ -14,16 +14,17 @@
  */
 package nl.lumc.sasc.biopet.extensions.igvtools
 
-import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Version }
 
 /**
  * General igvtools extension
  *
  * Created by wyleung on 5-1-15
  */
-abstract class IGVTools extends BiopetCommandLineFunction with Version {
-  executable = config("exe", default = "igvtools", namespace = "igvtools", freeVar = false)
-  def versionCommand = executable + " version"
+abstract class IGVTools extends BiopetJavaCommandLineFunction with Version {
+  jarFile = config("igvtools_jar", namespace = "igvtools")
+
+  def versionCommand = executable + s" -jar ${jarFile.getAbsolutePath} version"
   def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
   override def versionExitcode = List(0)
 }
\ No newline at end of file

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

@@ -76,25 +76,23 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
   }
 
   /** Returns command to execute */
-  def cmdLine = {
-    required(executable) +
-      required("count") +
-      optional("--maxZoom", maxZoom) +
-      optional("--windowSize", windowSize) +
-      optional("--extFactor", extFactor) +
-      optional("--preExtFactor", preExtFactor) +
-      optional("--postExtFactor", postExtFactor) +
-      optional("--windowFunctions", windowFunctions) +
-      optional("--strands", strands) +
-      conditional(bases, "--bases") +
-      optional("--query", query) +
-      optional("--minMapQuality", minMapQuality) +
-      conditional(includeDuplicates, "--includeDuplicates") +
-      conditional(pairs, "--pairs") +
-      required(input) +
-      required(outputArg) +
-      required(genomeChromSizes)
-  }
+  override def cmdLine = super.cmdLine +
+    required("count") +
+    optional("--maxZoom", maxZoom) +
+    optional("--windowSize", windowSize) +
+    optional("--extFactor", extFactor) +
+    optional("--preExtFactor", preExtFactor) +
+    optional("--postExtFactor", postExtFactor) +
+    optional("--windowFunctions", windowFunctions) +
+    optional("--strands", strands) +
+    conditional(bases, "--bases") +
+    optional("--query", query) +
+    optional("--minMapQuality", minMapQuality) +
+    conditional(includeDuplicates, "--includeDuplicates") +
+    conditional(pairs, "--pairs") +
+    required(input) +
+    required(outputArg) +
+    required(genomeChromSizes)
 
   /** This part should never fail, these values are set within this wrapper */
   private def outputArg: String = {

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -125,7 +125,7 @@ object CarpTest {
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "macs2" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test")
   )

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -194,6 +194,7 @@ object GentrapTest {
     "ribosome_refflat" -> (outputDir + File.separator + "ref.fa"),
     "varscan_jar" -> "test",
     "rscript" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "gatk_jar" -> "test"
   ) ++ Seq(
       // fastqc executables
@@ -203,7 +204,7 @@ object GentrapTest {
       // gentrap executables
       "cufflinks", "htseqcount", "grep", "pdflatex", "rscript", "tabix", "bgzip", "bedtoolscoverage", "md5sum",
       // bam2wig executables
-      "igvtools", "wigtobigwig"
+      "wigtobigwig"
     ).map { case exe => exe -> Map("exe" -> "test") }.toMap
 
   val sample1: Map[String, Any] = Map(

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -126,6 +126,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     "skip_metrics" -> skipMetrics,
     "skip_flexiprep" -> skipFlexiprep,
     "skip_markduplicates" -> skipMarkduplicates,
+    "paired" -> inputR2.isDefined,
     "aligner" -> aligner,
     "chunking" -> chunking,
     "number_of_chunks" -> (if (chunking) numberChunks.getOrElse(1) else None)

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -49,6 +49,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
     val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
     val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
+    val mappingExecuted = summary.getLibraryValues("mapping").nonEmpty
+    val pairedFound = !mappingExecuted || summary.getLibraryValues("mapping", "settings", "paired").exists(_._2 == Some(true))
     val flexiprepExecuted = summary.getLibraryValues("flexiprep")
       .exists { case ((sample, lib), value) => value.isDefined }
 
@@ -71,7 +73,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
         )) ++
-        (if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+        (if (pairedFound) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
         else Nil) ++
         (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -194,7 +194,7 @@ object MultisampleMappingTestTrait {
     "cutadapt" -> Map("exe" -> "test"),
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -210,7 +210,7 @@ object ShivaTest {
     "bwa" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "macs2" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test"),
     "bgzip" -> Map("exe" -> "test"),

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -134,7 +134,7 @@ object TinyCapTest {
     "cutadapt" -> Map("exe" -> "test"),
     "bowtie" -> Map("exe" -> "test"),
     "htseqcount" -> Map("exe" -> "test"),
-    "igvtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test")
   )