From 565f3979470d0cd82942d712c1cfcc19fbb73ff9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Jan 2016 12:46:39 +0100
Subject: [PATCH] Fixed rna metrics
---
.../pipelines/bammetrics/BamMetrics.scala | 3 --
.../biopet/extensions/bowtie/Bowtie2.scala | 4 +--
.../biopet/pipelines/gentrap/Gentrap.scala | 32 +++++++++----------
.../biopet/pipelines/mapping/Mapping.scala | 2 +-
4 files changed, 19 insertions(+), 22 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 1e00d04cc..01fd32ab2 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -39,7 +39,6 @@ class BamMetrics(val root: Configurable) extends QScript
var inputBam: File = _
/** Settings for CollectRnaSeqMetrics */
- var rnaMetricsSettings: Map[String, String] = Map()
var transcriptRefFlatFile: Option[File] = config("transcript_refflat")
/** return location of summary file */
@@ -107,8 +106,6 @@ class BamMetrics(val root: Configurable) extends QScript
rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
rnaMetrics.refFlat = transcriptRefFlatFile.get
- rnaMetrics.ribosomalIntervals = rnaMetricsSettings.get("ribosomal_intervals").collect { case n => new File(n) }
- rnaMetrics.strandSpecificity = rnaMetricsSettings.get("strand_specificity")
add(rnaMetrics)
addSummarizable(rnaMetrics, "rna")
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
index d84fde042..26a317561 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
@@ -2,10 +2,10 @@ package nl.lumc.sasc.biopet.extensions.bowtie
import java.io.File
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for bowtie 2
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 32afb9fd5..b4fd79d24 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
@@ -19,13 +19,13 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.picard.{MergeSamFiles, SortSam}
+import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{MergeTables, WipeReads}
-import nl.lumc.sasc.biopet.extensions.{HtseqCount, Ln}
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
+import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
-import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{CustomVarScan, Pdflatex, RawBaseCounter}
-import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap}
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config._
@@ -98,17 +98,6 @@ class Gentrap(val root: Configurable) extends QScript
/** Whether to do simple variant calling on RNA or not */
var callVariants: Boolean = config("call_variants", default = false)
- /** Settings for all Picard CollectRnaSeqMetrics runs */
- private def collectRnaSeqMetricsSettings: Map[String, String] = Map(
- "strand_specificity" -> (strandProtocol match {
- case NonSpecific => StrandSpecificity.NONE.toString
- case Dutp => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
- case otherwise => throw new IllegalStateException(otherwise.toString)
- })) ++ (ribosomalRefFlat match {
- case Some(rbs) => Map("ribosomal_intervals" -> rbs.toString)
- case None => Map()
- })
-
/** Default pipeline config */
override def defaults = Map(
"merge_strategy" -> "preprocessmergesam",
@@ -117,6 +106,17 @@ class Gentrap(val root: Configurable) extends QScript
"batch" -> 4,
"format" -> "sam"
),
+ "bammetrics" -> Map(
+ "transcript_refflat" -> annotationRefFlat,
+ "collectrnaseqmetrics" -> ((if (strandProtocol != null) Map(
+ "strand_specificity" -> (strandProtocol match {
+ case NonSpecific => StrandSpecificity.NONE.toString
+ case Dutp => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
+ case otherwise => throw new IllegalStateException(otherwise.toString)
+ })
+ )
+ else Map()) ++ (if (ribosomalRefFlat != null) ribosomalRefFlat.map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))
+ ),
"cutadapt" -> Map("minimum_length" -> 20),
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
"picard" -> Map(
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 6964fa24c..b04f7a58d 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -20,7 +20,7 @@ import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2, Bowtie}
+import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2, Bowtie }
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
--
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