Commit 8dee06e5 authored by wyleung's avatar wyleung
Browse files

Pipeline fixes

parent 64d1f13a
......@@ -111,7 +111,7 @@
<verbose>false</verbose>
<useNativeGit>true</useNativeGit>
<dotGitDirectory>${project.basedir}/../.git</dotGitDirectory>
<skipPoms>true</skipPoms>
<skipPoms>false</skipPoms>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
......
......@@ -8,7 +8,6 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge }
import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Clever }
......@@ -84,18 +83,18 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
mergeSamFiles.input = libraryBamfiles
mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
add(mergeSamFiles)
val bamIndex = SambambaIndex(root, mergeSamFiles.output)
add(bamIndex)
mergeSamFiles.output
} else null
val bamIndex = SambambaIndex(root, bamFile)
add(bamIndex)
/// bamfile will be used as input for the SV callers. First run Clever
// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
val cleverDir = svcallingDir + sampleID + ".clever/"
val clever = Clever(this, bamFile, this.reference, svcallingDir, cleverDir)
clever.deps = List(bamIndex.output)
sampleOutput.vcf += ("clever" -> List(clever.outputvcf))
add(clever)
......
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