0.5.0 (2025-01-15)
- remove deprecated functionality of
cubi-tk archive
- add
--filter-statusoption for controlling which landing zones are listed (#239) (900b67a) - add
cubi-tk sodar update-samplesheet(#240) (581e650) - Add common functions for interfacing with python-irodsclient (#202) (67e6e49)
- Add generic SODAR ingest command (#199) (8548c97)
- Add new command sodar landing-zone-validate (#219) (98e21c1)
- Adding cubi-tk snappy itransfer_sv_calling (#213) (5a00e40)
- allow varfish case resubmission (#224) (964bcac)
- irods download refactoring and new generic sodar downloader with preset for dragen data (#226 ) (#227) (3fc38af)
- presets for cubi-tk sodar ingest-fastq (#232 ) (#235) (8669118)
- Switching
cubi-tk sodar ingest-fastqfrom icommands to irods_common (#217) (cd9a3b9) - Update ingest-fastq, allow to match samples against assay table to determine collections names (#198) (#203) (8b3662d)
- adapt to varfish-cli >=0.6.2 syntax (#221) (9619609)
- isa-tab add-ped now only modifies values on process nodes of ped-supplied samples #207 (#233) (88977d4)
- parsing snappy config for with WGS projects (#231) (10592f3)
- varfish cli 06x uses new import syntax (#220) (#222) (cb10dbb)
- varfish-upload subprocess submission (#225) (0f7f5b2)
0.4.0 (2023-10-27)
- allow for existing files when using irods download (#176) (944a54c)
- Fast irods querying (#184) (d614fcc)
- Remove hardcoded snappy-pipeline steps (#174) (f171217)
- validate ISA-tabs after cookiecutter run (#181) (aeff82b)
- actually match files recursively (#180) (e9c49b6)
- add space between value and unit symbol for file size formatting (#166) (79e85bf)
- adjust to change in ISA-tab template (#186) (#187) (e4f46d4)
- allow mehari annotations (#189) (3939f83)
- archive copy hangs (#161) (ae8bb92)
- broken symlinks (#173) (f76e480)
- fix to snappy varfish-upload (#158) (dfebe77)
- Fixes for changes introdueced when switching pull functions to query (#188) (5fcc369)
- handling of <output_dir> input argument (#163) (bdf0e21)
- Unpin Mamba version in CI workflow (#193) (e5e5596)
- Update ISA-tpl dependencies (#195) (67e1f18)
- use increment, not sub-total, for tqdm.update (#182) (88672be)