From ca40d875c8ebbd1de440f26da56cf1ca1f1395d0 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Tue, 19 Jan 2016 11:57:11 +0100
Subject: [PATCH] move varscan wrapper to extensions
---
.../biopet/extensions/varscan}/fix_mpileup.py | 0
.../biopet/extensions/varscan/FixMpileup.scala | 12 ++++++++++++
.../variantcallers/VarscanCnsSingleSample.scala | 15 +++------------
3 files changed, 15 insertions(+), 12 deletions(-)
rename public/{shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/scripts => biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan}/fix_mpileup.py (100%)
create mode 100644 public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/scripts/fix_mpileup.py b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
similarity index 100%
rename from public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/scripts/fix_mpileup.py
rename to public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
new file mode 100644
index 000000000..827da73e3
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
@@ -0,0 +1,12 @@
+package nl.lumc.sasc.biopet.extensions.varscan
+
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by sajvanderzeeuw on 19-1-16.
+ */
+class FixMpileup(val root: Configurable) extends PythonCommandLineFunction {
+ setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/extensions/varscan/")
+ def cmdLine = getPythonCommand
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
index 896bdffd7..ddeba500e 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -2,12 +2,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.{ Ln, Tabix, Bgzip }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.varscan.VarscanMpileup2cns
+import nl.lumc.sasc.biopet.extensions.varscan.{ FixMpileup, VarscanMpileup2cns }
+import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
@@ -44,17 +42,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
writer.println(sample)
writer.close()
- val fixMpileup = new PythonCommandLineFunction {
- setPythonScript("fix_mpileup.py", "/nl/lumc/sasc/biopet/pipelines/shiva/scripts/")
- override val root: Configurable = this.root
- override def configName = "fix_mpileup"
- def cmdLine = getPythonCommand
- }
-
val varscan = new VarscanMpileup2cns(this)
varscan.vcfSampleList = Some(sampleFile)
- add(mpileup | fixMpileup | varscan | new Bgzip(this) > sampleVcf)
+ add(mpileup | new FixMpileup(this) | varscan | new Bgzip(this) > sampleVcf)
add(Tabix(this, sampleVcf))
sampleVcf
--
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