From ea9fe97777f08304a552292f6d148b535904ea64 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 19 Feb 2015 14:10:45 +0100
Subject: [PATCH] Changed executables for summary
---
.../sasc/biopet/core/summary/SummaryQScript.scala | 11 -----------
.../sasc/biopet/core/summary/WriteSummary.scala | 15 +++++++++++----
.../lumc/sasc/biopet/extensions/bwa/BwaMem.scala | 1 +
.../sasc/biopet/pipelines/mapping/Mapping.scala | 3 ++-
4 files changed, 14 insertions(+), 16 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 21704aa3e..f54eda7c8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -61,17 +61,6 @@ trait SummaryQScript extends BiopetQScript {
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles)
addChecksum(file)
- for ((_, sl) <- summarizables) {
- for (s <- sl) {
- s match {
- case c: BiopetCommandLineFunctionTrait => {
- executables += c.configName -> (new File(c.executable), c.getVersion)
- }
- case _ =>
- }
- }
- }
-
for ((_, file) <- this.summaryFiles)
addChecksum(file)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index fac1055e3..c73cc0505 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -48,10 +48,17 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val pipelineMap = {
val files = parseFiles(qscript.summaryFiles)
val settings = qscript.summarySettings
- val executables = {
- for ((name, (file, version)) <- qscript.executables) yield {
- name -> Map("version" -> version, "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(file.getCanonicalPath, "N/A"))
- }
+ val executables: Map[String, Any] = {
+ (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
+ f match {
+ case f: BiopetCommandLineFunctionTrait => {
+ f.configName -> Map("version" -> f.getVersion,
+ "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
+ }
+ case _ => throw new IllegalStateException("This should not be possible")
+ }
+
+ }).toMap
}
val map = Map(qscript.summaryName -> ((if (settings.isEmpty) Map[String, Any]() else Map("settings" -> settings)) ++
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 74cdad0ce..731cdc278 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BwaMem(val root: Configurable) extends Bwa {
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 3ee791dc2..d7e125f3f 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -94,7 +94,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
- def summaryFiles = Map()
+ def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1) ++
+ (if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
def summarySettings = Map(
"skip_metrics" -> skipMetrics,
--
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