From 64134d4609a7bdd887812f8ec192f0f5dd5c25ad Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 29 Jan 2016 14:05:45 +0100
Subject: [PATCH] wgs and rna metrics now got config value to enable/disable
them
---
.../biopet/pipelines/bammetrics/BamMetrics.scala | 15 ++++++++-------
.../extensions/picard/CollectRnaSeqMetrics.scala | 2 +-
.../sasc/biopet/pipelines/gentrap/Gentrap.scala | 8 ++++----
.../pipelines/gentrap/scripts/PlotHeatmap.scala | 2 +-
4 files changed, 14 insertions(+), 13 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 01fd32ab2..78bf5f309 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
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.File
+import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
@@ -31,16 +32,15 @@ class BamMetrics(val root: Configurable) extends QScript
with SummaryQScript
with SampleLibraryTag
with Reference
- with TargetRegions {
+ with TargetRegions
+ with AnnotationRefFlat
+ with RibosomalRefFlat {
def this() = this(null)
@Input(doc = "Bam File", shortName = "BAM", required = true)
var inputBam: File = _
- /** Settings for CollectRnaSeqMetrics */
- var transcriptRefFlatFile: Option[File] = config("transcript_refflat")
-
/** return location of summary file */
def summaryFile = (sampleId, libId) match {
case (Some(s), Some(l)) => new File(outputDir, s + "-" + l + ".BamMetrics.summary.json")
@@ -92,7 +92,7 @@ class BamMetrics(val root: Configurable) extends QScript
add(gcBiasMetrics)
addSummarizable(gcBiasMetrics, "gc_bias")
- if (transcriptRefFlatFile.isEmpty) {
+ if (config("wgs_metrics", default = true)) {
val wgsMetrics = new CollectWgsMetrics(this)
wgsMetrics.input = inputBam
wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".wgs.metrics")
@@ -100,12 +100,13 @@ class BamMetrics(val root: Configurable) extends QScript
addSummarizable(wgsMetrics, "wgs")
}
- if (transcriptRefFlatFile.isDefined) {
+ if (config("rna_metrics", default = false)) {
val rnaMetrics = new CollectRnaSeqMetrics(this)
rnaMetrics.input = inputBam
rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
- rnaMetrics.refFlat = transcriptRefFlatFile.get
+ rnaMetrics.refFlat = annotationRefFlat()
+ rnaMetrics.ribosomalIntervals = ribosomalRefFlat()
add(rnaMetrics)
addSummarizable(rnaMetrics, "rna")
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 2aca96da6..29c3ef7aa 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -36,7 +36,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
var refFlat: File = null
@Input(doc = "Location of rRNA sequences in interval list format", required = false)
- var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
+ var ribosomalIntervals: Option[File] = None
@Output(doc = "Output metrics file", required = true)
var output: File = null
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 455bbd9c9..043cd83dc 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
@@ -93,12 +93,12 @@ class Gentrap(val root: Configurable) extends QScript
"merge_strategy" -> "preprocessmergesam",
"gsnap" -> Map(
"novelsplicing" -> 1,
- "batch" -> 4,
- "format" -> "sam"
+ "batch" -> 4
),
"shivavariantcalling" -> Map("variantcallers" -> List("varscan_cns_singlesample")),
"bammetrics" -> Map(
- "transcript_refflat" -> annotationRefFlat,
+ "wgs_metrics" -> false,
+ "rna_metrics" -> true,
"collectrnaseqmetrics" -> ((if (strandProtocol.isSet) Map(
"strand_specificity" -> (strandProtocol() match {
case StrandProtocol.NonSpecific => StrandSpecificity.NONE.toString
@@ -106,7 +106,7 @@ class Gentrap(val root: Configurable) extends QScript
case otherwise => throw new IllegalStateException(otherwise.toString)
})
)
- else Map()) ++ (if (ribosomalRefFlat.isSet) ribosomalRefFlat().map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))
+ else Map()))
),
"cutadapt" -> Map("minimum_length" -> 20),
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
index 998ece67c..decd56a55 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
@@ -43,7 +43,7 @@ class PlotHeatmap(val root: Configurable) extends RscriptCommandLineFunction {
(if (useLog) Seq("-L") else Seq()) ++
(countType match {
case Some(t) => Seq("-C", t)
- case _ => Seq()
+ case _ => Seq()
}) ++
Seq("-I", input.getAbsolutePath, "-O", output.getAbsolutePath)
}
--
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