Mercurial > repos > elixir-it > mutect2

diff mutect2.xml @ 8:467fcccde14d draft

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Uploaded
author elixir-it
date Thu, 25 Oct 2018 04:44:53 -0400
parents 2ebf2cd4f18f
children a517190d2b3d
line wrap: on
line diff
--- a/mutect2.xml	Tue Jul 03 04:46:13 2018 -0400
+++ b/mutect2.xml	Thu Oct 25 04:44:53 2018 -0400
@@ -44,7 +44,7 @@
       ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
       ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned
       gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ;
-      java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
+      java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct 4  -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
       #if $reference_source.reference_source_selector == "history"
       -R genome.fa
       #end if