# HG changeset patch
# User elixir-it
# Date 1540457093 14400
# Node ID 467fcccde14d2aecaf89a43c9504a487d767b847
# Parent  2ebf2cd4f18fb19fbacf67209dc3407698fb523b
Uploaded

diff -r 2ebf2cd4f18f -r 467fcccde14d .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Thu Oct 25 04:44:53 2018 -0400
@@ -0,0 +1,10 @@
+categories:
+- Variant Analysis
+description: 'MuTect2:somatic SNP and indel caller'
+homepage_url: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php
+long_description: |
+MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller.
+name: MuTect2
+owner: elixir-it
+remote_repository_url: https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper
+type: unrestricted
diff -r 2ebf2cd4f18f -r 467fcccde14d mutect2.xml
--- 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