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Update command line help to include -qcset option #32

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Nov 16, 2018
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Update command line help to include -qcset option #32

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9 changes: 7 additions & 2 deletions scripts/ds-cgpwgs.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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)
Expand Down Expand Up @@ -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
Expand Down