From a7b9890fc5c13abf3c98776c08ab15103aa81b32 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 13 Mar 2015 10:11:04 +0100
Subject: [PATCH] Use correct flag annotations for Picard CollectRnaSeqMetrics
---
.../extensions/picard/CollectRnaSeqMetrics.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
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 d95f18f16..6629fae64 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
@@ -34,11 +34,14 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
@Input(doc = "Gene annotations in refFlat form", required = true)
var refFlat: File = null
+ @Input(doc = "Location of rRNA sequences in interval list format", required = false)
+ var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
+
@Output(doc = "Output metrics file", required = true)
var output: File = null
- @Argument(doc = "Location of rRNA sequences in interval list format", required = false)
- var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
+ @Output(doc = "PDF output of the coverage chart", required = false)
+ var chartOutput: Option[File] = config("chart_output")
@Argument(doc = "Strand specificity", required = false)
var strandSpecificity: Option[String] = config("strand_specificity")
@@ -46,9 +49,6 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
@Argument(doc = "Minimum length of transcripts to use for coverage-based values calculation", required = false)
var minimumLength: Option[Int] = config("minimum_length")
- @Argument(doc = "PDF output of the coverage chart", required = false)
- var chartOutput: Option[File] = config("chart_output")
-
@Argument(doc = "Sequences to ignore for mapped reads", required = false)
var ignoreSequence: Option[String] = config("ignore_sequence")
--
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