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CHANGELOG.md

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Changelog

1.11.0 2022-05-09

  • Nanopore data: allows new result structure with barcode alignment file and 'other reports' folder (requires core-utils-lib 1.11.0 or later)
  • Nanopore data: introduces map to remove log files that should not be saved dependent on different datamover origins
  • Fix for nanopore: data without unclassified reads does not lead to error upon registration
  • Ptx mass spec data: change msconvert server

1.10.0 2021-07-26

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

1.9.0 2021-06-28

  • 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)

1.8.0 2021-05-11

  • Add example Java dropbox

1.7.0 2021-03-19

  • Provides fully tested functionality to register generic imaging data, with OMERO server support (v5.4.10). Link to PR
  • 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

1.6.0 2021-01-22

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

1.5.0 2020-11-03

  • New maintenance task: update missing checksum once, after dss starts.
  • Fix for nanopore registration: rename folders for pooling case
  • Fix for experiment update: force identifier into a string to support v3 API objects

1.4.1 2020-11-03

  • Imgag dropbox: raise an exception, if files of unknown type are part of the transaction

1.4.0

  • Provide first imaging registration support with OMERO server
  • Provide environment.yaml that can be used to configure a conda environment for the proper setup for the register-omero-metadata dropbox
  • Register unclassified pooling data of Nanopore experiments directly at the experiment level (no copies are added to sample-based datasets)
  • Add description for data of register-hlatyping-dropbox

1.3.1

  • Avoid sample registration for existing mass spectrometry data

1.3

  • Provide metadata schema in JSON for the IMGAG dropbox
  • Register checksums for Oxford Nanopore datasets
  • Register unclassified read data for Oxford Nanopore datasets

1.2

  • Provide ETL routine for Oxford Nanopore NGS data
  • New dropbox register-nanopore-dropbox