Release 1.14.1

What's Changed

• handle extra basecalling folder by @wow-such-code in #106
• Fix/omero issues by @wow-such-code in #107
• Feature/nanopore parser v4 by @wow-such-code in #109
• add error handling via email for attachment upload by @wow-such-code in #111
• Sync dev by @luiskuhn in #113
• Use new default sequencer name for Illumina data, removing the specific model by @wow-such-code in #114
• next release by @wow-such-code in #115
• sync master by @luiskuhn in #116
• handle new nanopore structure with pod5 and some optional folders by @wow-such-code in #117
• sync dev into omero56 by @luiskuhn in #119
• Etl script to register pair of raw and mzml files without conversion by @wow-such-code in #118
• prepare for production by @wow-such-code in #121
• fix issue for .d folders and missing accession by @wow-such-code in #122
• ETL upgrade (omero56 update/ required ETL features) by @luiskuhn in #120
• Prepare release to production by @wow-such-code in #123
• Register Pac Bio data by @wow-such-code in #125
• add information for pacbio and preconverted mass spec data by @wow-such-code in #126
• prepare next version for deployment by @wow-such-code in #127
• Patch: upgrade-omero56 by @luiskuhn in #128
• deploy omero56-patch by @luiskuhn in #129
• remove between-sample offset and correctly check for existing samples by @wow-such-code in #131
• handle additional data variablity by @wow-such-code in #134
• Disable sample tracking by @KochTobi in #135

New Contributors

• @KochTobi made their first contribution in #135

Full Changelog: 1.14.0...1.14.1

Version 1.14.0

prepare release (#112)

* add error handling via email for attachment upload (#111)

* update readme for attachment upload

Patch release 1.13.1

• Fixes minor issue with simultaneous registration of fastq and vcf files
• Fixes debug prints causing errors due to concatenation

Release 1.13.0

• Enables registration of new version of nanopore data including extra basecalling folder
• Fixes mistake in readme for imaging data registration
• Makes imaging data registration error handling compatible with old python/jython versions

Minor release 1.12.0

Logs duplicate MTB dataset registration but does not cause manual intervention anymore.

Chocolate Macaron

Prepare release 1.11.0 (#96)

* change ms conversion server

* remove some log files dependent on origin lab (#95)

Co-authored-by: Tobias Koch <[email protected]>

* handle data without unclassified reads

* Update CL (#92)

Co-authored-by: Tobias Koch <[email protected]>
Co-authored-by: Sven F <[email protected]>

The dark knight returns

• Provides new ETL for MTB project data that are not supposed to be stored in QUK17 (#89)
• Allow multiple sequencing lanes for MTB data

The dark ETL rises

• Provides new ETL routine written in Java, that will replace all Jython scripts at some point (#85)
• Support for nf-core pipeline result registration (#85)
• Provides metadata validation for imaging data (OMERO etl). (#85)

Spring Roll

• Add example Java dropbox

From 1.7.0:

• Provides fully tested functionality to register generic imaging data, with OMERO server support (v5.4.10).
• Uses an omero-importer-cli (with Bio-formats) for image file registration into an OMERO server instance
• Uses an initial version of the openBIS-OMERO metadata model

Blue Moon

• Fix for workflow result registration: fetch sample by identifier instead of search service
• Retry sample tracking updates twice and log failures that occur