Mercurial > repos > elixir-it > vep86_vcf2maf

diff vep_unico.xml @ 2:bfd92976550f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Thu, 25 Oct 2018 04:46:04 -0400
parents 7a54ac4976d0
children ca1e48c52db9
line wrap: on
line diff
--- a/vep_unico.xml	Mon Oct 01 11:21:05 2018 -0400
+++ b/vep_unico.xml	Thu Oct 25 04:46:04 2018 -0400
@@ -29,7 +29,7 @@
 	
 	#if str($veptools.veptoolsselect) =="annotate"
 	 perl \$CONDA_DEFAULT_ENV/bin/variant_effect_predictor.pl
-        --fork \${GALAXY_SLOTS:-4}
+        --fork 4
         --offline
         --dir \$CONDA_DEFAULT_ENV/vep_cache
         --force_overwrite
@@ -57,7 +57,8 @@
             --vep-path \$CONDA_DEFAULT_ENV/bin/
             --vep-data \$CONDA_DEFAULT_ENV/vep_cache
             --ref-fasta $veptools.reference
-            --species $veptools.species;
+            --species $veptools.species
+	    --filter-vcf 0 ;
 
         #end if
 		 ]]>