From fc2af339904e89de82e9c27d1830b56c2214db77 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Sep 2015 15:10:52 +0200
Subject: [PATCH] Still executes multisample jobs when all samples are given
with --sample flag
---
.../main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 2 +-
.../nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala | 2 +-
3 files changed, 4 insertions(+), 4 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 91b265986..c84c9faa8 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
@@ -87,8 +87,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
this match {
- case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
- logger.info("Write summary is skipped because sample flag is used")
+ case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+ logger.info("Write report is skipped because sample flag is used")
case _ => reportClass.foreach(add(_))
}
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 baf9f5acb..17631709f 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
@@ -131,7 +131,7 @@ trait MultiSampleQScript extends SummaryQScript {
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
- if (onlySamples.isEmpty) {
+ if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
addMultiSampleJobs()
} else onlySamples.foreach(sampleId => samples.get(sampleId) match {
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 1876c2fb0..7f0fce673 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
@@ -136,7 +136,7 @@ trait SummaryQScript extends BiopetQScript {
addChecksum(file)
this match {
- case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+ case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write summary is skipped because sample flag is used")
case _ => add(writeSummary)
}
--
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