Merge pull request #309 from wtsi-npg/devel

pull from devel to master to create Release 3.23.0

Changes

@@ -1,3 +1,10 @@
+
+Release 3.23.0 (2024-07-25)
+
+ - Add PACBIO_ISOSEQ_PRIMERS to Metadata - required for archiving
+   analysis output from IsoSeq analysis jobs
+ - Add fastq and gff as a standard ancillary file type
+
 Release 3.22.2 (2024-05-24)
 
  - Add iRODS 4.3.2, remove 4.3-nightly

lib/WTSI/NPG/iRODS/Annotator.pm

@@ -72,7 +72,7 @@ sub hts_data_suffixes {
 =cut
 
 sub hts_ancillary_suffixes {
-  return (qw[bam_stats bcfstats bamcheck bed bqsr_table fasta flagstat hops json quant 
+  return (qw[bam_stats bcfstats bamcheck bed bqsr_table fasta fastq flagstat gff hops json quant 
              seqchksum stats tab txt xml _SamHaplotag_Clear_BC _SamHaplotag_UnClear_BC _SamHaplotag_Missing_BC_QT_tags
             ]
          );

lib/WTSI/NPG/iRODS/Metadata.pm

@@ -69,6 +69,7 @@ our @EXPORT = qw(
                   $PACBIO_COLLECTION_NUMBER
                   $PACBIO_DATA_LEVEL
                   $PACBIO_INSTRUMENT_NAME
+                  $PACBIO_ISOSEQ_PRIMERS
                   $PACBIO_MULTIPLEX
                   $PACBIO_PLATE_NUMBER
                   $PACBIO_PRODUCTION
@@ -186,6 +187,7 @@ our $PACBIO_CELL_INDEX         = 'cell_index';
 our $PACBIO_COLLECTION_NUMBER  = 'collection_number';
 our $PACBIO_DATA_LEVEL         = 'data_level';
 our $PACBIO_INSTRUMENT_NAME    = 'instrument_name';
+our $PACBIO_ISOSEQ_PRIMERS     = 'isoseq_primers';
 our $PACBIO_MULTIPLEX          = 'multiplex';
 our $PACBIO_PLATE_NUMBER       = 'plate_number';
 our $PACBIO_PRODUCTION         = 'production';
@@ -250,7 +252,7 @@ Keith James <[email protected]>
 
 =head1 COPYRIGHT AND DISCLAIMER
 
-Copyright (C) 2015, 2016, 2017, 2018, 2023 Genome Research Limited.
+Copyright (C) 2015 - 2018, 2023, 2024 Genome Research Limited.
 All Rights Reserved.
 
 This program is free software: you can redistribute it and/or modify