From 99485cfd0ff360a191299babee8f25e2986d132a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 15 Oct 2015 10:32:24 +0200
Subject: [PATCH] Fix picard versions
---
.../sasc/biopet/extensions/picard/Picard.scala | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index a20869a4e..1517e3d93 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -95,15 +95,15 @@ object Picard extends Logging {
logger.debug("dependencies: " + dependencies)
- val htsjdk = dependencies.find(dep => dep("groupId") == "samtools" && dep("artifactId") == "htsjdk").collect {
- case dep =>
- "samtools htsjdk " + dep("version")
- }
-
- dependencies.find(dep => dep("groupId") == "picard" && dep("artifactId") == "picard").collect {
- case dep =>
- "Picard " + dep("version") + " using " + htsjdk.getOrElse("unknown htsjdk")
- }
+ val htsjdk = dependencies.find(dep =>
+ (dep("groupId") == "com.github.samtools" || dep("groupId") == "samtools") &&
+ dep("artifactId") == "htsjdk")
+ .collect { case dep => "samtools htsjdk " + dep("version") }
+
+ dependencies.find(dep =>
+ (dep("groupId") == "com.github.broadinstitute" || dep("groupId") == "picard") &&
+ dep("artifactId") == "picard")
+ .collect { case dep => "Picard " + dep("version") + " using " + htsjdk.getOrElse("unknown htsjdk") }
case otherwise => None
}
}
--
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