From e93bf522d797121189b64c2d0640b55dcc14bb7e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 8 Oct 2015 10:44:10 +0200
Subject: [PATCH] Added samtoolsview options to fixedvalues
---
.../nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 2be78c722..fb9004103 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
-import nl.lumc.sasc.biopet.extensions.picard.{BuildBamIndex, MergeSamFiles}
+import nl.lumc.sasc.biopet.extensions.picard.{ BuildBamIndex, MergeSamFiles }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
@@ -46,7 +46,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
),
"samtoolsview" -> Map("q" -> 10)
)
-
+
+ override def fixedValues = Map(
+ "samtoolsview" -> Map(
+ "h" -> true,
+ "b" -> true
+ )
+ )
+
def summaryFile = new File(outputDir, "Carp.summary.json")
//TODO: Add summary
@@ -122,8 +129,6 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val samtoolsView = new SamtoolsView(qscript)
samtoolsView.input = bamFile
samtoolsView.output = bamFileFilter
- samtoolsView.b = true
- samtoolsView.h = true
add(samtoolsView)
val buildBamIndex = new BuildBamIndex(qscript)
--
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