v0.7.0

0.7.0 (2025-09-24)

Breaking Changes

Several commands have been renamed, set for deprecation or removed:

• Renamed cubi-tk sodar ingest-fastq to cubi-tk sodar ingest-data (now more descriptive)
• Renamed cubi-tk sodar ingest to cubi-tk sodar ingest-collection (now more descriptive)
• Renamed cubi-tk sodar pull-data-collection to cubi-tk sodar pull-data (now more descriptive)
• Renamed cubi-tk sodar landing-zone-create to cubi-tk sodar create-landingzone (acts on project, not LZ)
• Renamed cubi-tk sodar landing-zone-list to cubi-tk sodar list-landingzones (acts on project, not LZ)
• Deprecating cubi-tk sodar pull-raw-data
• Deprecating cubi-tk sea-snap check-irods
• Removed cubi-tk snappy kickoff
• Removed cubi-tk isa-tab resolve-hpo and cubi-tk isa-tab annotate
• Removed cubi-tk org-raw and cubi-tk irods

All ingest and itransfer functions now use an harmonised cli interface with the same options, some of which have been replaced or renamed:

• --parallel-checksum-jobs replaces --num-parallel-transfers (same functionality, better name)
• --sync removed in favor of --overwrite {mode=sync}

Additions

• Documentation has been updated and future-proofed with CI test build
• Usage of ~/.cubitkrc.toml has been updated and now allows switching between different Sodar instances
• Most cubi-tk fucntions have been updated to work with multi-assay Sodar projects and have improved handling of assay (and landingzone) selection
• The cli interface for ingest and itransfer functions has new options:
  • --overwrite {mode=sync} allows seelction of overwrite behavior. The new default (sync) is to only overwrite remote files when the local one has a different file size
  • --dry-run added: only print a list of transfers
  • --select-lz added: allows interactive selection of landingzone

Features

• add cubi-tk sodar deletion-requests (#297) (8edec81)
• changes for onko data upload (#289) (f20401c)
• introduce and refactor SodarIngestBase incl harmonised options (#295) (6d15d9b)
• major cubi-tk refactoring (#283) (1a5397d)
• update docs (#309) (5f34d4f)
• update ingest-data for wgs germline (#301) (3316e9b)

Bug Fixes

• (Sodar)API POST calls need to use the data field, not params (#288) (ce7388b)
• add defaults for --output-directory in snappy pull-data commands (#302) (e581861)
• bug fix val in feat removed thats needed (#290) (971c12f)
• call altamisa with typer, fixes #249 (#279) (70f8667)
• dict needs items keyword (#287) (fa2333d)
• dont gen checksum for checksums (#293) (1d8fe5b)
• get assay UUID pull data (#285) (f121236)
• nicer json output for LZ commands, always write this json to stdout, better test (#303) (bd1414a)
• refactored function didn't retrun anything (#286) (01c849b)
• replaced deprecated logger with loguru (#273) (d065ae9)
• resolve merge issues from SodarIngestBase and deletion-request changes (#300) (80ab2b7)
• retrun last found match col (#292) (1655670)
• set assay uuid from lz (#307) (cf869dc)
• switch sodar profile with different irods_env (#284) (cf73749)