From ec347f6de261af143718b67f4edf0dbf761c2544 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 16 Apr 2015 13:33:15 +0200
Subject: [PATCH] Added rna metrics
---
.../sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 10 ++++++++++
.../extensions/picard/CollectRnaSeqMetrics.scala | 7 ++++---
2 files changed, 14 insertions(+), 3 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 8c94ac09c..affed4885 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
@@ -38,6 +38,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
/** Bed of amplicon that is used */
var ampliconBedFile: Option[File] = config("amplicon_bed")
+ var rnaMetrics: Boolean = config("rna_metrcis", default = false)
+
/** return location of summary file */
def summaryFile = (sampleId, libId) match {
case (Some(sampleId), Some(libId)) => new File(outputDir, sampleId + "-" + libId + ".BamMetrics.summary.json")
@@ -70,6 +72,14 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
add(CollectGcBiasMetrics(this, inputBam, outputDir))
+ if (rnaMetrics) {
+ 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"))
+ add(rnaMetrics)
+ }
+
case class Intervals(bed: File, intervals: File)
// Create temp jobs to convert bed files to intervals lists
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index dd922fce5..10708d6ff 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -32,7 +32,8 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
var input: File = null
@Input(doc = "Gene annotations in refFlat form", required = true)
- var refFlat: File = null
+ var refFlat: File = config("refFlat")
+ //TODO: RefFlat could break gentrap, needs to be checked
@Input(doc = "Location of rRNA sequences in interval list format", required = false)
var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
@@ -99,9 +100,9 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
required("STRAND_SPECIFICITY=", strandSpecificity, spaceSeparated = false) +
required("MINIMUM_LENGTH=", minimumLength, spaceSeparated = false) +
required("CHART_OUTPUT=", chartOutput, spaceSeparated = false) +
- repeat("IGNORE_SEQUENCE=", ignoreSequence, spaceSeparated = false) +
+ optional("IGNORE_SEQUENCE=", ignoreSequence, spaceSeparated = false) +
required("RRNA_FRAGMENT_PERCENTAGE=", rRNAFragmentPercentage, spaceSeparated = false) +
- repeat("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated = false) +
+ optional("METRIC_ACCUMULATION_LEVEL=", metricAccumulationLevel, spaceSeparated = false) +
required("REFERENCE_SEQUENCE=", referenceSequence, spaceSeparated = false) +
required("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
required("STOP_AFTER=", stopAfter, spaceSeparated = false)
--
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