diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala index 8a14292a1e73381b2c7135cef8520ca9810cdaf6..f44ec38c91e33f6eac073c2d1726b06bf6fde701 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala +++ b/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) } } } diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala index 606287478b432a0806bf900c082dbda7e4f4d9a0..3c5dc47bcf747e9630d7d40d5608b4dd1670d7f6 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala +++ b/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) } } } diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala index 7589d9f86cb9e5369fc1b4bd199b629012b7e74b..221b062b35ce4d911239b292a3b285cae3a26bfd 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala +++ b/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") diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala index ff6fb17d0b3adeccfb1d364ceacf2a67fb7f4862..c83ee46b7ee50cfb6ace76d29b4eef6880282beb 100644 --- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala +++ b/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) } }