From 002c7f8f926269cbce7706a84b438570d1cd658e Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 29 Jan 2015 10:26:07 +0100
Subject: [PATCH] bug fixes in carp pipeline
---
.../sasc/biopet/pipelines/carp/Carp.scala | 33 +++++++++++++++----
1 file changed, 26 insertions(+), 7 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 c03b4252f..a69ec4d32 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
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.carp
import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
@@ -53,18 +54,30 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
runSamplesJobs
- //val macs2 = new Macs2CallPeak(this)
- //macs2.treatment = new File("patient.bam")
- //macs2.control = new File("control.bam")
+ for (sample <- getSamples) {
+ val controls: List[String] = config("control", sample = sample, default = Nil)
+
+ for (control <- controls) {
+ if (!getSamples.exists(_ == control))
+ throw new IllegalStateException("For sample: " + sample + " this control: " + control + " does not exist")
+ val macs2 = new Macs2CallPeak(this)
+ macs2.treatment = samplesOutput(sample).mappedBamFile
+ macs2.control = samplesOutput(control).mappedBamFile
+ macs2.name = sample + "_VS_" + control
+ macs2.outputdir = globalSampleDir + sample + "/" + "macs2/" + macs2.name + "/"
+ add(macs2)
+ }
+ }
}
def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
val sampleOutput = new SampleOutput
- val sampleID: String = sampleConfig("ID").toString
+ val sampleID: String = getCurrentSample
+ val sampleDir = globalSampleDir + sampleID + "/"
sampleOutput.libraries = runLibraryJobs(sampleConfig)
val bamfiles = sampleOutput.libraries.map(_._2.mappedBamFile).toList
- sampleOutput.mappedBamFile = new File(globalSampleDir + sampleID + "/" + sampleID + ".bam")
+ sampleOutput.mappedBamFile = new File(sampleDir + sampleID + ".bam")
if (bamfiles.length == 1) {
add(Ln(this, bamfiles.head, sampleOutput.mappedBamFile))
val oldIndex = new File(bamfiles.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
@@ -78,14 +91,20 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
add(merge)
}
+ val macs2 = new Macs2CallPeak(this)
+ macs2.treatment = sampleOutput.mappedBamFile
+ macs2.name = sampleID
+ macs2.outputdir = sampleDir + "macs2/" + macs2.name + "/"
+ add(macs2)
+
return sampleOutput
}
def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
val libraryOutput = new LibraryOutput
- val runID: String = runConfig("ID").toString
- val sampleID: String = sampleConfig("ID").toString
+ val runID: String = getCurrentLibrary
+ val sampleID: String = getCurrentSample
val runDir: String = globalSampleDir + sampleID + "/run_" + runID + "/"
if (runConfig.contains("R1")) {
--
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