Adding genral config for MultiSampleMapping

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

@@ -37,7 +37,7 @@ trait TemplateTool extends ToolCommand {
 
   def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any]
 
-  val sampleConfigs: List[File] = Nil
+  lazy val sampleConfigs: List[File] = Nil
 
 }
 

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -15,7 +15,7 @@
 package nl.lumc.sasc.biopet
 
 import nl.lumc.sasc.biopet.core.PipelineStatus
-import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
 
 object BiopetExecutableMain extends BiopetExecutable {
   def pipelines: List[MainCommand] = List(
@@ -44,5 +44,8 @@ object BiopetExecutableMain extends BiopetExecutable {
 
   def tools: List[MainCommand] = PipelineStatus :: BiopetToolsExecutable.tools
 
-  def templates: List[MainCommand] = List()
+  def templates: List[MainCommand] = List(
+    nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,
+    nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
+  )
 }

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala

+package nl.lumc.sasc.biopet.pipelines.mapping.template
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Reference, TemplateTool}
+import nl.lumc.sasc.biopet.utils.Question
+
+/**
+  * Created by pjvanthof on 17/12/2016.
+  */
+object MultiSampleMapping extends TemplateTool {
+
+  override lazy val sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
+
+  def possibleAligners = List("bwa-mem", "bwa-aln", "bowtie", "bowtie2", "gsnap", "hisat2",
+    "tophat", "stampy", "star", "star-2pass")
+
+  def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any] = {
+    val referenceConfig = map ++ Reference.askReference
+
+    val aligner = if (map.contains("aligner")) map("aligner").toString
+    else  Question.string("Aligner", posibleValues = possibleAligners, default = Some("bwa-mem"))
+
+    referenceConfig ++ Map(
+      "aligner" -> aligner
+      )
+  }
+}

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala

@@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.shiva.template
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, TemplateTool}
+import nl.lumc.sasc.biopet.core.TemplateTool
+import nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping
 import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.Question
 
@@ -11,19 +12,24 @@ import nl.lumc.sasc.biopet.utils.Question
   */
 object Shiva extends TemplateTool {
 
-  override val sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
+  override lazy val sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
 
   def possibleVariantcallers: List[String] = {
     ShivaVariantcalling.callersList(null).map(_.name)
   }
 
   def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any] = {
-    map ++ Reference.askReference ++
-      Map(
-        "variantcallers" -> Question.list("Variantcallers", posibleValues = possibleVariantcallers,
-          default = Some(List("haplotypecaller_gvcf", "haplotypecaller"))),
-        "use_indel_realigner" -> Question.boolean("use_indel_realigner", default = Some(true)),
-        "use_base_recalibration" -> Question.boolean("use_base_recalibration", default = Some(true))
+    val mappingConfig = MultiSampleMapping.pipelineMap(map, expert)
+
+    val variantCallers = Question.list("Variantcallers", posibleValues = possibleVariantcallers,
+      default = Some(List("haplotypecaller_gvcf", "haplotypecaller")))
+    val useIndelRealigner = Question.boolean("Use indel realigner", default = Some(true))
+    val useBaseRecalibration = Question.boolean("Use base recalibration", default = Some(true))
+
+    mappingConfig ++ Map(
+      "variantcallers" -> variantCallers,
+      "use_indel_realigner" -> useIndelRealigner,
+      "use_base_recalibration" -> useBaseRecalibration
       )
   }
 }