From 1f620a44248da526c4c7a4fc1275b68923dd99ad Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 Feb 2015 14:54:13 +0100
Subject: [PATCH] Make all module within one qscript
---
.../sasc/biopet/core/summary/SummaryQScript.scala | 2 +-
.../sasc/biopet/core/summary/WriteSummary.scala | 14 +++++++-------
2 files changed, 8 insertions(+), 8 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 46583bad8..3efd77ec3 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
@@ -41,7 +41,7 @@ trait SummaryQScript extends BiopetQScript with Summarizable {
def addSummaryJobs: Unit = {
val writeSummary = new WriteSummary(this)
- addSummarizable(this, summaryName)
+ addSummarizable(this, "pipeline")
//Automatic checksums
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles) {
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 e7bcb9f3e..c686109ce 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
@@ -19,20 +19,20 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
require(root.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
- val summaryQScript = root.asInstanceOf[SummaryQScript]
+ val qscript = root.asInstanceOf[SummaryQScript]
@Input(doc = "deps", required = false)
var deps: List[File] = Nil
@Output(doc = "Summary output", required = true)
- var out: File = summaryQScript.summaryFile
+ var out: File = qscript.summaryFile
var md5sum: Boolean = config("summary_md5", default = true)
//TODO: add more checksums types
override def freezeFieldValues(): Unit = {
- for (q <- summaryQScript.summaryQScripts) deps :+= q.summaryFile
- for ((_, l) <- summaryQScript.summarizables; s <- l) s match {
+ for (q <- qscript.summaryQScripts) deps :+= q.summaryFile
+ for ((_, l) <- qscript.summarizables; s <- l) s match {
case f: QFunction => deps :+= f.firstOutput
case _ =>
}
@@ -44,10 +44,10 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
def run(): Unit = {
val map = (for (
- ((name, sampleId, libraryId), summarizables) <- summaryQScript.summarizables;
+ ((name, sampleId, libraryId), summarizables) <- qscript.summarizables;
summarizable <- summarizables
) yield {
- val map = Map(name -> parseSummarizable(summarizable))
+ val map = Map(qscript.summaryName ->Map(name -> parseSummarizable(summarizable)))
(sampleId match {
case Some(sampleId) => Map("samples" -> Map(sampleId -> (libraryId match {
@@ -58,7 +58,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
}, (v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
}).foldRight(Map[String, Any]())((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
- val combinedMap = (for (qscript <- summaryQScript.summaryQScripts) yield {
+ val combinedMap = (for (qscript <- qscript.summaryQScripts) yield {
ConfigUtils.fileToConfigMap(qscript.summaryFile)
}).foldRight(map)((a, b) => ConfigUtils.mergeMaps(a, b))
--
GitLab