From 71426017618eff511288b2827ff85c944858d640 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 14:17:49 +0200
Subject: [PATCH] Added the -T arg
---
.../nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
index cb1f72d8d..3ec14161a 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -27,10 +27,11 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
prefix = config("prefix", default = new File(Files.createTempDir(), output.getAbsolutePath))
}
- def cmdLine = executable + required("sort") +
+ def cmdLine = required(executable) + required("sort") +
optional("-m", (coreMemeory + "G")) +
optional("-@", threads) +
optional("-O", outputFormat) +
+ required("-T", prefix) +
conditional(sortByName, "-n") +
(if (outputAsStsout) "" else required("-o", output)) +
(if (inputAsStdin) "" else required(input))
--
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