From adc3523872df29405e1741eaa2dfa2a67e61a51d Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 19 Feb 2021 11:00:46 +0100
Subject: [PATCH] fix sage
---
hmftools.wdl | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 3fe845a..49e4eeb 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -590,9 +590,7 @@ task Sage {
}
command {
- java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
- -cp /usr/local/share/hmftools-sage-2.2-2/sage.jar \
- com.hartwig.hmftools.sage.SageApplication \
+ SAGE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-tumor ~{tumorName} \
-tumor_bam ~{tumorBam} \
~{"-reference " + normalName} \
--
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