From 8dee06e5885cebaf83bca9282a8529520b672678 Mon Sep 17 00:00:00 2001
From: wyleung <w.y.leung@e-sensei.nl>
Date: Fri, 24 Oct 2014 16:20:08 +0200
Subject: [PATCH] Pipeline fixes
---
biopet-framework/pom.xml | 2 +-
.../nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala | 9 ++++-----
2 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/biopet-framework/pom.xml b/biopet-framework/pom.xml
index c66afeb48..70fbf74f9 100644
--- a/biopet-framework/pom.xml
+++ b/biopet-framework/pom.xml
@@ -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>
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index b647ab4ed..16460f0fd 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -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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