2.43.0

release 2.43.0

2.31.1

release 2.31.1

2.24.1

• Order Conda channels for tests so that NPG channels have highest priority
  and conda-forge the lowest.

2.13.0

• WTSI::NPG::HTS::Illumina::ResultSet - added geno to genotype_regex.
• WTSI::NPG::HTS::Illumina::ResultSet - added quant.zip to ancillary_regex.
• WTSI::NPG::HTS::Illumina::ResultSet - added _target_autosome.stats to ancillary_regex.
• WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher - archive tag zero file.
• Control caching of st::api::lims objects to reduce memory use in highly plexed runs. WTSI::NPG::HTS::LIMSFactory now uses Cache::LRU to limit the number of cached st::api::lims objects to 100.
• Added BioNano Saphyr run publisher and run publishing script

release 2.9.2

• register RunParameters.xml file for Illumina run publishing
• when publishing cram files, only publish crai (not bai)

2.8.1

use tears 1.2.4 (-w flag now required for write to iRODS)

2.8

• switched to disposable-irods 1.3 (iRODS packages from Sanger S3,
  replaced RENCI FTP site)
• added single-server option
• added support for data files to change during the tar process
  and to detect and archive those changes
• individually check the checksum of files local to the gridionxi
  where they are loaded and compare with the iRODS checksum
• updated the samtools and htslib versions to 1.7
• added tar file auditor
• use manifest checksums to confirm file contents
• support loading PacBio RSII files created using out of date reagents
• allow a user-supplied checksum to be used in TarPublisher and TarStream
  (so GridIONRunPublisher can allow the checksum of uncompressed data to be used)
• publish fastq files during the catchup phase
• allow auditing of older GridION tar files which used a relative path for tarred files
• archiving changes for illumina sequencing genotype files
• fix for the regex used when choosing to ignore files
• minor fix to DataObjectFactory.pm

2.7

• Moved quant file tests to illumina run publisher tests
• Added compression extensions to illumina ancillary file regular expression
• Added tag hops files to illumina run publisher tests

2.6

• extended log publisher find command to include STAR aligner log files
• add 'STAR' as a valid aligner to the header parser
• make file formats 'tab' and 'zip' have restricted access
• add compress suffixes to ancillary lane/plex file patterns

2.5

• Refactored BioNano publication, with metadata from MLWH
• Add file type option in PacBio meta updater
• Added a configurable local output directory
• GridION: ancillary files and metadata; configurable TMPDIR