diff --git a/bin/populate_wtsi_irods_groups.pl b/bin/populate_wtsi_irods_groups.pl index 28df6b5b..d3aad0b2 100755 --- a/bin/populate_wtsi_irods_groups.pl +++ b/bin/populate_wtsi_irods_groups.pl @@ -146,8 +146,8 @@ sub _uid_to_irods_uid { my $study_id = $study->id_study_lims; my $dag_str = $study->data_access_group || q(); my $is_seq = $study->iseq_flowcells->count || - $study->pac_bio_runs->count; - + $study->pac_bio_runs->count || + $study->oseq_flowcells->count; $log->debug("Working on study $study_id, SScape data access: '$dag_str'"); my @members; diff --git a/lib/WTSI/NPG/iRODS/Annotator.pm b/lib/WTSI/NPG/iRODS/Annotator.pm index f04e62f9..a0e06002 100644 --- a/lib/WTSI/NPG/iRODS/Annotator.pm +++ b/lib/WTSI/NPG/iRODS/Annotator.pm @@ -72,7 +72,7 @@ sub hts_data_suffixes { =cut sub hts_ancillary_suffixes { - return (qw[bam_stats bamcheck bed fasta flagstat hops json quant seqchksum stats tab txt xml]); + return (qw[bam_stats bcfstats bamcheck bed fasta flagstat hops json quant seqchksum stats tab txt xml]); } =head2 hts_genotype_suffixes diff --git a/lib/WTSI/NPG/iRODS/Metadata.pm b/lib/WTSI/NPG/iRODS/Metadata.pm index 05bd3e28..cb60de77 100644 --- a/lib/WTSI/NPG/iRODS/Metadata.pm +++ b/lib/WTSI/NPG/iRODS/Metadata.pm @@ -61,6 +61,9 @@ our @EXPORT = qw( $GBS_PLEX_NAME + $COMPOSITION + $COMPONENT + $PACBIO_CELL_INDEX $PACBIO_COLLECTION_NUMBER $PACBIO_INSTRUMENT_NAME @@ -169,6 +172,10 @@ our $YHUMAN = 'yhuman'; # Genotyping by Sequencing (Illumina) our $GBS_PLEX_NAME = 'gbs_plex'; +# Composition JSON string for merged data +our $COMPOSITION = 'composition'; +our $COMPONENT = 'component'; + # PacBio our $PACBIO_CELL_INDEX = 'cell_index'; our $PACBIO_COLLECTION_NUMBER = 'collection_number'; @@ -236,7 +243,8 @@ Keith James =head1 COPYRIGHT AND DISCLAIMER -Copyright (C) 2015, 2016 Genome Research Limited. All Rights Reserved. +Copyright (C) 2015, 2016, 2017, 2018 Genome Research Limited. All +Rights Reserved. This program is free software: you can redistribute it and/or modify it under the terms of the Perl Artistic License or the GNU General