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pull from devel to master to create Release 3.23.0 #309

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merged 6 commits into from
Jul 25, 2024
Merged

pull from devel to master to create Release 3.23.0 #309

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4072cfd
Add PACBIO_ISOSEQ_PRIMERS to Metadata
ces Jun 4, 2024
a1962a1
Merge pull request #306 from ces/pacbio2
kjsanger Jun 5, 2024
0fa5a0b
Add fastq and gff as a standard ancillary file type
ces Jun 6, 2024
43f219f
Merge pull request #307 from ces/pacbio3
kjsanger Jun 7, 2024
bd3344c
prep release 3.23.0
jmtcsngr Jul 25, 2024
c9b332e
Merge pull request #308 from jmtcsngr/devel
jmtcsngr Jul 25, 2024
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7 changes: 7 additions & 0 deletions Changes
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Original file line number Diff line number Diff line change
@@ -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
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2 changes: 1 addition & 1 deletion lib/WTSI/NPG/iRODS/Annotator.pm
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Expand Up @@ -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
]
);
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4 changes: 3 additions & 1 deletion lib/WTSI/NPG/iRODS/Metadata.pm
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Expand Up @@ -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
Expand Down Expand Up @@ -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';
Expand Down Expand Up @@ -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
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