Merge pull request #32 from zhouyangyu/patch-1

Update command line help to include -qcset option

scripts/ds-cgpwgs.pl

@@ -267,11 +267,11 @@ sub ref_unpack {
 
 =head1 NAME
 
-dh-wrapper.pl - Generate the param file and execute analysisWGS.sh (for dockstore)
+dh-cgpwgs.pl - Generate the param file and execute analysisWGS.sh (for dockstore)
 
 =head1 SYNOPSIS
 
-dh-wrapper.pl [options] [file(s)...]
+dh-cgpwgs.pl [options] [file(s)...]
 
   Required parameters:
     -reference   -r   Path to core reference tar.gz
@@ -285,6 +285,7 @@ =head1 SYNOPSIS
     -nidx             Normal [CR|B]AM index (bai|csi|crai)
     -exclude     -e   Exclude these contigs from SNV/Indel analysis
                         e.g. NC_007605,hs37d5,GL%
+    -qcset       -qc  Path to qcGenotype*.tar.gz
 
   Optional parameters
     -species     -sp  Species name (may require quoting)
@@ -341,6 +342,10 @@ =head1 OPTION DETAILS
 
 Contigs to be excluded from Pindel analysis, csv, use '%' for wildcard.
 
+=item B<-qcset>
+
+Path to qcGenotype*.tar.gz
+
 =item B<-species>
 
 Specify overriding species, by default will select the most prevelant entry in