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changeset 83:9995d7db92ff draft

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fixed the second vcf input
author stef
date Mon, 23 Mar 2015 07:45:44 -0400
parents b17c87f56422
children b641568b1500
files falco-filter-report.xml falco/bin/falco-filter-report
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/falco-filter-report.xml	Mon Mar 23 07:31:08 2015 -0400
+++ b/falco-filter-report.xml	Mon Mar 23 07:45:44 2015 -0400
@@ -7,7 +7,7 @@
     
   </requirements>
 
-  <description>FALCO Report: Amplicon Analysis Pipeline</description>
+  <description>FALCO Amplicon Analysis Pipeline Reporting</description>
 
   <command interpreter="bash">
     falco-filter-report.sh $falco_cfg;
--- a/falco/bin/falco-filter-report	Mon Mar 23 07:31:08 2015 -0400
+++ b/falco/bin/falco-filter-report	Mon Mar 23 07:45:44 2015 -0400
@@ -76,7 +76,7 @@
 
 if ( defined($vcfOther) ){
 	print STDOUT localtime() . " [$$] converting vcf to tsv\n";
-	system( "$vcf2tsv $vcf > $base\.Other\.tsv" );
+	system( "$vcf2tsv $vcfOther > $base\.Other\.tsv" );
 	print STDOUT localtime() . " [$$] splitting vcf columns\n";
 	system( "$spliteff $base\.Other\.tsv Other >> $base\.res\.tsv" );
 }