From b2a7573b51ba30e8bb7c577621ec5bc32f0ad8f8 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 15:28:25 +0100
Subject: [PATCH] Make sample-level metrics optional, instead of library-level
metrics (for RNA)
---
.../biopet/pipelines/gentrap/Gentrap.scala | 30 +++++++++----------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 739b80437..4ece0c105 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -640,9 +640,11 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
job
}
- /** Picard CollectRnaSeqMetrics job */
- private lazy val collectRnaSeqMetricsJob: CollectRnaSeqMetrics =
- makeCollectRnaSeqMetricsJob(alnFile, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
+ /** Picard CollectRnaSeqMetrics job, only when library > 1 */
+ private lazy val collectRnaSeqMetricsJob: Option[CollectRnaSeqMetrics] = (libraries.size > 1)
+ .option {
+ makeCollectRnaSeqMetricsJob(alnFileDirty, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
+ }
private def wipeJob: Option[WipeReads] = removeRibosomalReads
.option {
@@ -694,9 +696,11 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
addPerLibJobs()
// merge or symlink per-library alignments
add(sampleAlnJob)
- // general RNA-seq metrics
- add(collectRnaSeqMetricsJob)
- addSummarizable(collectRnaSeqMetricsJob, "rna_metrics")
+ // general RNA-seq metrics, if there are > 1 library
+ collectRnaSeqMetricsJob match {
+ case Some(j) => add(j); addSummarizable(j, "rna_metrics")
+ case None => ;
+ }
// add strand-specific jobs if defined
alnPlusStrandJobs.foreach(_.addAllJobs())
alnMinusStrandJobs.foreach(_.addAllJobs())
@@ -740,10 +744,8 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def alnFile: File = mappingJob.outputFiles("finalBamFile")
/** Library-level RNA-seq metrics job, only when we have more than 1 library in the sample */
- def collectRnaSeqMetricsJob: Option[CollectRnaSeqMetrics] = (Sample.this.libraries.size > 1)
- .option {
- makeCollectRnaSeqMetricsJob(alnFile, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
- }
+ def collectRnaSeqMetricsJob: CollectRnaSeqMetrics =
+ makeCollectRnaSeqMetricsJob(alnFile, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
/** Per-library mapping job */
def mappingJob: Mapping = {
@@ -761,11 +763,9 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def addJobs(): Unit = {
// create per-library alignment file
addAll(mappingJob.functions)
- // create RNA metrics job, if defined
- collectRnaSeqMetricsJob match {
- case Some(j) => add(j); addSummarizable(j, "rna_metrics")
- case None => ;
- }
+ // create RNA metrics job
+ add(collectRnaSeqMetricsJob)
+ addSummarizable(collectRnaSeqMetricsJob, "rna_metrics")
qscript.addSummaryQScript(mappingJob)
}
--
GitLab