From ad73824fde8950bc9068704a3cc99d7200c07b9c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Sep 2015 14:58:11 +0200
Subject: [PATCH] Fix summary when --sample flag is used in multisample
pipelines
---
.../main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 6 +++++-
.../scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 2 +-
.../nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala | 6 +++++-
3 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index f35c07a0a..91b265986 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -86,7 +86,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
- reportClass.foreach(add(_))
+ this match {
+ case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+ logger.info("Write summary is skipped because sample flag is used")
+ case _ => reportClass.foreach(add(_))
+ }
Logging.checkErrors()
}
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 d8756c7b9..baf9f5acb 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
@@ -26,7 +26,7 @@ trait MultiSampleQScript extends SummaryQScript {
qscript =>
@Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
- private val onlySamples: List[String] = Nil
+ private[core] val onlySamples: List[String] = Nil
require(globalConfig.map.contains("samples"), "No Samples found in config")
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 52c77fe8a..1876c2fb0 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -135,7 +135,11 @@ trait SummaryQScript extends BiopetQScript {
for ((_, file) <- this.summaryFiles)
addChecksum(file)
- add(writeSummary)
+ this match {
+ case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+ logger.info("Write summary is skipped because sample flag is used")
+ case _ => add(writeSummary)
+ }
}
}
--
GitLab