Merge pull request #178 from wtsi-npg/devel

release 3.3.0 prep : merge devel to master

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;

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

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 <[email protected]>
 
 =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