fix typo

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

@@ -35,13 +35,13 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
         sample = sample + "_bd")
 
-      val compresssedVCF = new SortVcf(this)
-      compresssedVCF.input = bdvcf.output
-      compresssedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = bdvcf.output
+      compressedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
 
-      add(bdcfg, breakdancer, bdvcf, compresssedVCF)
+      add(bdcfg, breakdancer, bdvcf, compressedVCF)
 
-      addVCF(sample, compresssedVCF.output)
+      addVCF(sample, compressedVCF.output)
     }
   }
 }

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

@@ -37,12 +37,12 @@ class Clever(val root: Configurable) extends SvCaller {
       cleverVCF.isIntermediate = true
       add(cleverVCF)
 
-      val sortvcf = new SortVcf(this)
-      sortvcf.input = cleverVCF.output
-      sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
-      add(sortvcf)
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = cleverVCF.output
+      compressedVCF.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
+      add(compressedVCF)
 
-      addVCF(sample, sortvcf.output)
+      addVCF(sample, compressedVCF.output)
     }
   }
 }

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

@@ -43,12 +43,12 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
         add(delly)
 
-        val compresssedVCF = new SortVcf(this)
-        compresssedVCF.input = delly.outputvcf
-        compresssedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
-        add(compresssedVCF)
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
+        add(compressedVCF)
 
-        catVariants.variant :+= compresssedVCF.output
+        catVariants.variant :+= compressedVCF.output
       }
       if (dup) {
         val delly = new DellyCaller(this)
@@ -57,12 +57,12 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
         add(delly)
 
-        val compresssedVCF = new SortVcf(this)
-        compresssedVCF.input = delly.outputvcf
-        compresssedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
-        add(compresssedVCF)
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
+        add(compressedVCF)
 
-        catVariants.variant :+= compresssedVCF.output
+        catVariants.variant :+= compressedVCF.output
       }
       if (inv) {
         val delly = new DellyCaller(this)
@@ -71,12 +71,12 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
         add(delly)
 
-        val compresssedVCF = new SortVcf(this)
-        compresssedVCF.input = delly.outputvcf
-        compresssedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
-        add(compresssedVCF)
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
+        add(compressedVCF)
 
-        catVariants.variant :+= compresssedVCF.output
+        catVariants.variant :+= compressedVCF.output
       }
       if (tra) {
         val delly = new DellyCaller(this)
@@ -85,12 +85,12 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
         add(delly)
 
-        val compresssedVCF = new SortVcf(this)
-        compresssedVCF.input = delly.outputvcf
-        compresssedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
-        add(compresssedVCF)
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
+        add(compressedVCF)
 
-        catVariants.variant :+= compresssedVCF.output
+        catVariants.variant :+= compressedVCF.output
       }
 
       require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")

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

@@ -59,12 +59,12 @@ class Pindel(val root: Configurable) extends SvCaller {
       pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
       add(pindelVcf)
 
-      val compresssedVCF = new SortVcf(this)
-      compresssedVCF.input = pindelVcf.outputVCF
-      compresssedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
-      add(compresssedVCF)
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = pindelVcf.outputVCF
+      compressedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
+      add(compressedVCF)
 
-      addVCF(sample, compresssedVCF.output)
+      addVCF(sample, compressedVCF.output)
     }
 
   }