changeset 9:a517190d2b3d draft

Uploaded

--- a/.shed.yml	Thu Oct 25 04:44:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-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

--- a/mutect2.xml	Thu Oct 25 04:44:53 2018 -0400
+++ b/mutect2.xml	Sat Sep 21 13:21:54 2019 -0400
@@ -38,13 +38,13 @@
 
       ##TODO creation of .dict file of the genome required by mutect2 to run
       #if $reference_source.reference_source_selector == "history"
-      java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
+      java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
       #end if
 
       ##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
+      ##and move the .jar file to \$CONDA_PREFIX/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 4  -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
+      java -jar \$CONDA_PREFIX/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

--- a/tool-data/mutect2_indexes.loc.sample	Thu Oct 25 04:44:53 2018 -0400
+++ b/tool-data/mutect2_indexes.loc.sample	Sat Sep 21 13:21:54 2019 -0400
@@ -32,4 +32,3 @@
 #is the value stored in the workflow for that parameter. That is why the
 #hg19 entry above looks odd. New genomes can be better-looking.
 #
-hg38	hg38	hg38_GDC	/export/gatkhg38pl/GRCh38.d1.vd1.fa