Added to generateIndexes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala

@@ -42,9 +42,8 @@ class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with
   var localftabchars: Option[Int] = config("localftabchars")
   var seed: Option[Int] = config("seed")
 
-  var large-index: Boolean = config("large-index", default = false)
-  var dcv: Boolean = config("dcv", default = false)
-  var memory-fitting: Boolean = config("memory-fitting", default = false)
+  var largeIndex: Boolean = config("large_index", default = false)
+  var memoryFitting: Boolean = config("memory_fitting", default = false)
   var nodc: Boolean = config("nodc", default = false)
   var noref: Boolean = config("noref", default = false)
   var justref: Boolean = config("justref", default = false)
@@ -70,9 +69,8 @@ class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with
     optional("--haplotype", haplotype) +
     optional("--ss", ss) +
     optional("--exon", exon) +
-    conditional(large-index, "--large-index") +
-    conditional(dcv, "--dcv") +
-    conditional(memory-fitting, "--memory-fitting") +
+    conditional(largeIndex, "--large-index") +
+    conditional(memoryFitting, "--memory-fitting") +
     conditional(nodc, "--nodc") +
     conditional(noref, "--noref") +
     conditional(justref, "--justref") +

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala

@@ -14,16 +14,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.generateindexes
 
-import java.io.{ File, PrintWriter }
+import java.io.{File, PrintWriter}
 import java.util
 
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
 import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2Build, BowtieBuild}
 import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
+import nl.lumc.sasc.biopet.extensions.hisat.Hisat2Build
 import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -267,6 +268,17 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
           "bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
         )
 
+        // Hisat2 index
+        val hisat2Index = new Hisat2Build(this)
+        hisat2Index.inputFasta = createLinks(new File(genomeDir, "hisat2"))
+        hisat2Index.hisat2IndexBase = new File(new File(genomeDir, "hisat2"), "reference").getAbsolutePath
+        add(hisat2Index)
+        configDeps :+= hisat2Index.jobOutputFile
+        outputConfig += "hisat2" -> Map(
+          "reference_fasta" -> hisat2Index.inputFasta.getAbsolutePath,
+          "hisat_index" -> hisat2Index.inputFasta.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
+        )
+
         val writeConfig = new WriteConfig
         writeConfig.deps = configDeps
         writeConfig.out = new File(genomeDir, s"$speciesName-$genomeName.json")

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexesTest.scala

@@ -102,6 +102,7 @@ object GenerateIndexesTest {
   val config = Map("output_dir" -> outputDir,
     "bwa" -> Map("exe" -> "test"),
     "star" -> Map("exe" -> "test"),
+    "hisat2build" -> Map("exe" -> "test"),
     "bowtiebuild" -> Map("exe" -> "test"),
     "bowtie2build" -> Map("exe" -> "test"),
     "gmapbuild" -> Map("exe" -> "test"),