From bbaa6236e019d683024257dc9e9773abf25a554a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 13:33:00 +0100
Subject: [PATCH] Add per-library RNA metrics job when the sample contains more
than 1 library
---
.../biopet/pipelines/gentrap/Gentrap.scala | 47 ++++++++++++-------
1 file changed, 31 insertions(+), 16 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 a635d4dc4..fa80426f2 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
@@ -279,6 +279,24 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
job
}
+ /** General function to create CollectRnaSeqMetrics job, for per-sample and per-library runs */
+ protected def makeCollectRnaSeqMetricsJob(alnFile: File, outMetrics: File,
+ outChart: Option[File] = None): CollectRnaSeqMetrics = {
+ val job = new CollectRnaSeqMetrics(qscript)
+ job.input = alnFile
+ job.output = outMetrics
+ job.refFlat = annotationRefFlat
+ job.chartOutput = outChart
+ job.assumeSorted = true
+ job.strandSpecificity = strandProtocol match {
+ case NonSpecific => Option(StrandSpecificity.NONE.toString)
+ case Dutp => Option(StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString)
+ case _ => throw new IllegalStateException
+ }
+ job.ribosomalIntervals = ribosomalRefFlat
+ job
+ }
+
/** Steps to run before biopetScript */
def init(): Unit = {
// TODO: validate that exons are flattened or not (depending on another option flag?)
@@ -338,7 +356,6 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Summary files of the sample */
def summaryFiles: Map[String, File] = Map(
"alignment" -> alnFile,
- "metrics" -> collectRnaSeqMetricsJob.output
) ++ Map(
"gene_fragments_count" -> geneFragmentsCount,
"exon_fragments_count" -> exonFragmentsCount,
@@ -621,21 +638,8 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
}
/** Picard CollectRnaSeqMetrics job */
- private def collectRnaSeqMetricsJob: CollectRnaSeqMetrics = {
- val job = new CollectRnaSeqMetrics(qscript)
- job.input = alnFile
- job.output = createFile(".rna_metrics")
- job.refFlat = annotationRefFlat
- job.chartOutput = Option(createFile(".coverage_bias.pdf"))
- job.assumeSorted = true
- job.strandSpecificity = strandProtocol match {
- case NonSpecific => Option(StrandSpecificity.NONE.toString)
- case Dutp => Option(StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString)
- case _ => throw new IllegalStateException
- }
- job.ribosomalIntervals = ribosomalRefFlat
- job
- }
+ private lazy val collectRnaSeqMetricsJob: CollectRnaSeqMetrics =
+ makeCollectRnaSeqMetricsJob(alnFile, createFile(".rna_metrics"), Option(createFile(".coverage_bias.pdf")))
private def wipeJob: Option[WipeReads] = removeRibosomalReads
.option {
@@ -732,6 +736,12 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Alignment results of this library ~ can only be accessed after addJobs is run! */
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")))
+ }
+
/** Per-library mapping job */
def mappingJob: Mapping = {
val job = new Mapping(qscript)
@@ -748,6 +758,11 @@ 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 => ;
+ }
qscript.addSummaryQScript(mappingJob)
}
--
GitLab