Merge branch 'fix-delly' into 'develop'

Sortvcf on the end



See merge request !468

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
 import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
 import nl.lumc.sasc.biopet.extensions.picard.SortVcf
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caller delly */
@@ -33,69 +34,60 @@ class Delly(val root: Configurable) extends SvCaller {
       val dellyDir = new File(outputDir, sample)
 
       val catVariants = new CatVariants(this)
-      catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz")
+      catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
+      catVariants.isIntermediate = true
 
       if (del) {
         val delly = new DellyCaller(this)
         delly.input = bamFile
         delly.analysistype = "DEL"
+        delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
         add(delly)
 
-        val compressedVCF = new SortVcf(this)
-        compressedVCF.input = delly.outputvcf
-        compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
-        add(compressedVCF)
-
-        catVariants.variant :+= compressedVCF.output
+        catVariants.variant :+= delly.outputvcf
       }
       if (dup) {
         val delly = new DellyCaller(this)
         delly.input = bamFile
         delly.analysistype = "DUP"
+        delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
         add(delly)
 
-        val compressedVCF = new SortVcf(this)
-        compressedVCF.input = delly.outputvcf
-        compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
-        add(compressedVCF)
-
-        catVariants.variant :+= compressedVCF.output
+        catVariants.variant :+= delly.outputvcf
       }
       if (inv) {
         val delly = new DellyCaller(this)
         delly.input = bamFile
         delly.analysistype = "INV"
+        delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
         add(delly)
 
-        val compressedVCF = new SortVcf(this)
-        compressedVCF.input = delly.outputvcf
-        compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
-        add(compressedVCF)
-
-        catVariants.variant :+= compressedVCF.output
+        catVariants.variant :+= delly.outputvcf
       }
       if (tra) {
         val delly = new DellyCaller(this)
         delly.input = bamFile
         delly.analysistype = "TRA"
+        delly.isIntermediate = true
         delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
         add(delly)
 
-        val compressedVCF = new SortVcf(this)
-        compressedVCF.input = delly.outputvcf
-        compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
-        add(compressedVCF)
-
-        catVariants.variant :+= compressedVCF.output
+        catVariants.variant :+= delly.outputvcf
       }
 
-      require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")
+      if (catVariants.variant.isEmpty) Logging.addError("At least 1 SV-type should be selected for Delly")
 
       add(catVariants)
-      addVCF(sample, catVariants.outputFile)
+
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = catVariants.outputFile
+      compressedVCF.output = catVariants.outputFile + ".gz"
+      add(compressedVCF)
+
+      addVCF(sample, compressedVCF.output)
     }
   }
 }

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

@@ -130,7 +130,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
 
     pipeline.inputBams = Map("bam" -> ShivaSvCallingTest.inputTouch("bam" + ".bam"))
 
-    if (!del && !dup && !inv && !tra) intercept[IllegalArgumentException] {
+    if (!del && !dup && !inv && !tra) intercept[IllegalStateException] {
       pipeline.init()
       pipeline.script()
     }