From e2769135fe900b2acabde394cdff3bfdce4f3fc2 Mon Sep 17 00:00:00 2001 From: Joe Zhou Date: Thu, 16 Aug 2018 12:46:00 -0400 Subject: [PATCH] Update command line help to include -qcset option --- scripts/ds-cgpwgs.pl | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/scripts/ds-cgpwgs.pl b/scripts/ds-cgpwgs.pl index a0f0313..4c1b901 100644 --- a/scripts/ds-cgpwgs.pl +++ b/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