From 7e1495dcd4ed1dcdae5973e93c46f330da5ffa7a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Oct 2015 13:45:39 +0100
Subject: [PATCH] Implemented sample specific settings in the summary
---
.../sasc/biopet/core/MultiSampleQScript.scala | 6 +++++
.../biopet/core/summary/WriteSummary.scala | 22 +++++++++++++++----
2 files changed, 24 insertions(+), 4 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index f60aeeca8..81c992b4d 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -35,6 +35,9 @@ trait MultiSampleQScript extends SummaryQScript {
/** Overrules config of qscript with default sample */
val config = new ConfigFunctions(defaultSample = sampleId)
+ /** Sample specific settings */
+ def summarySettings: Map[String, Any] = Map()
+
/** Library class with basic functions build in */
abstract class AbstractLibrary(val libId: String) extends Summarizable {
/** Overrules config of qscript with default sample and default library */
@@ -45,6 +48,9 @@ trait MultiSampleQScript extends SummaryQScript {
qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
}
+ /** Library specific settings */
+ def summarySettings: Map[String, Any] = Map()
+
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
if (nameRegex.findFirstIn(libId) == None)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 7b8f34ecb..3af28669c 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, BiopetJavaCommandLineFunction, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
@@ -99,12 +99,26 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
).toMap
}
- val map = Map(qscript.summaryName -> ((if (settings.isEmpty) Map[String, Any]() else Map("settings" -> settings)) ++
- (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map("pipeline" -> files))) ++
- (if (executables.isEmpty) Map[String, Any]() else Map("executables" -> executables.toMap))))
+ val map = Map(qscript.summaryName -> (Map(
+ "settings" -> settings,
+ "files" -> Map("pipeline" -> files),
+ "executables" -> executables.toMap))
+ )
qscript match {
case tag: SampleLibraryTag => prefixSampleLibrary(map, tag.sampleId, tag.libId)
+ case q:MultiSampleQScript => {
+ q.samples.map { case (sampleName,sample) =>
+ sampleName -> Map(
+ qscript.summaryName -> Map("settings" -> sample.summarySettings),
+ "libraries" -> sample.libraries.map { case (libName, lib) =>
+ sampleName -> Map(
+ qscript.summaryName -> Map("settings" -> lib)
+ )
+ }
+ )
+ } ++ map
+ }
case _ => map
}
}
--
GitLab