From 0d14a49a8e8c4c70186abf5c4c5a63a722856a46 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 May 2016 11:26:05 +0200
Subject: [PATCH] Adding gtf download
---
.../generateindexes/GenerateIndexes.scala | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
index 5041dbb55..1f39db6b2 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -196,6 +196,21 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
outputConfig += "dbsnp" -> cv.out
}
+ val gtfFile: Option[File] = genomeConfig.get("gtf_uri").map { gtfUri =>
+ val curl = new Curl(this)
+ curl.url = gtfUri.toString
+ curl.output = new File(annotationDir, new File(curl.url).getName)
+ add(curl)
+ outputConfig += "annotation_gtf" -> curl.output
+ curl.output
+ }
+
+ val refFlatFile: Option[File] = gtfFile.map { gtf =>
+ val refFlat = new File(gtf + ".refFlat")
+ //TODO: gtf to refFlat conversion
+ refFlat
+ }
+
// Bwa index
val bwaIndex = new BwaIndex(this)
bwaIndex.reference = createLinks(new File(genomeDir, "bwa"))
--
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