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bihealth
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cubi-tk
CUBI Tooling for SODAR, VarFish et al.
MIT License
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fix: allow mehari annotations
#189
holtgrewe
closed
1 year ago
0
fix: Fixes for changes introdueced when switching pull functions to query
#188
Nicolai-vKuegelgen
closed
1 year ago
2
fix: adjust to change in ISA-tab template (#186)
#187
holtgrewe
closed
1 year ago
1
Sub command "snappy pull-sheets" broken with latest DNA sequencing ISA-tab template
#186
holtgrewe
closed
1 year ago
0
Should `irods check` validate the stored data or against the md5 file
#185
xiamaz
opened
1 year ago
4
feat: Fast irods querying
#184
xiamaz
closed
1 year ago
5
Integrate snappy pull-data into workflow configuration
#183
xiamaz
opened
1 year ago
0
fix: use increment, not sub-total, for tqdm.update
#182
sellth
closed
1 year ago
1
feat: validate ISA-tabs after cookiecutter run
#181
sellth
closed
1 year ago
3
fix: actually match files recursively
#180
sellth
closed
1 year ago
1
chore: release 0.4.0
#179
github-actions[bot]
closed
1 year ago
1
Validate output of `cubi-tk isa-tpl`
#178
sellth
closed
1 year ago
0
Do not require a pipeline-job.sh for each pipeline step when using snappy kickoff
#177
xiamaz
opened
1 year ago
0
feat: allow for existing files when using irods download
#176
xiamaz
closed
1 year ago
3
Allow pull-raw-data to work without force-overwriting data
#175
xiamaz
closed
1 year ago
0
feat: Remove hardcoded snappy-pipeline steps
#174
xiamaz
closed
1 year ago
7
fix: broken symlinks
#173
sellth
closed
1 year ago
1
Replace `logzero` as logging solution
#172
sellth
opened
1 year ago
1
docs: recommend newer python
#171
sellth
closed
1 year ago
1
refactor!: Move ISA-Tab templates into a separate repository (#96)
#170
mikkonie
closed
1 year ago
4
Old Python version
#169
sellth
closed
1 year ago
0
feat: SODAR ingest command based on irods-pythonclient
#168
sellth
closed
1 year ago
2
tqdm progress bar broken
#167
sellth
closed
1 year ago
0
fix: add space between value and unit symbol for file size formatting
#166
sellth
closed
1 year ago
7
`cubi-tk snappy`is not yet adapted to new/renamed snappy steps
#165
Nicolai-vKuegelgen
closed
1 year ago
1
`cubi-tk snappy pull-sheets` has undocumented samplehseet requirements
#164
Nicolai-vKuegelgen
opened
1 year ago
2
fix: handling of <output_dir> input argument
#163
sellth
closed
1 year ago
3
improve `cubi-tk isa-tpl` output dir handling
#162
sellth
closed
1 year ago
0
fix: archive copy hangs
#161
ericblanc20
closed
1 year ago
2
archive copy hangs
#160
ericblanc20
closed
1 year ago
0
chore: release 0.3.1
#159
github-actions[bot]
closed
1 year ago
0
fix: fix to snappy varfish-upload
#158
holtgrewe
closed
1 year ago
1
ci: move to conventional commits & release-please
#157
holtgrewe
closed
1 year ago
1
Added --first-batch and --last-batch options to `cubi-tk snappy pull-sheets` (#154)
#156
Nicolai-vKuegelgen
closed
1 year ago
4
cubi-tk snappy pull-raw-data is slow for large studies
#155
holtgrewe
closed
1 year ago
1
cubi-tk snappy pull-sheets needs a --min-version
#154
holtgrewe
closed
1 year ago
0
Isatpl ssc
#153
Nicolai-vKuegelgen
closed
1 year ago
0
Bump wheel from 0.30.0 to 0.38.1 in /requirements
#152
dependabot[bot]
closed
1 year ago
0
Remove prospector from requirements (#150)
#151
eudesbarbosa
closed
1 year ago
1
Remove `prospector` from requirements
#150
eudesbarbosa
closed
1 year ago
0
Adding support for Sniffles2 to varfish-upload (#148)
#149
holtgrewe
closed
1 year ago
0
Add support for minimap2.sniffles2 to varfish-upload
#148
holtgrewe
closed
1 year ago
0
Added unit test for snappy pull-sheets
#147
eudesbarbosa
closed
1 year ago
1
Accommodate cookiecutter templates repository
#146
eudesbarbosa
closed
1 year ago
0
Fixed bug in `isa-tpl` output directory path argument (#142)
#145
eudesbarbosa
closed
2 years ago
0
`snappy kickoff`: update workflow dependency (#143)
#144
eudesbarbosa
closed
1 year ago
0
Update workflow dependency in `snappy kickoff`
#143
eudesbarbosa
closed
1 year ago
0
isa-tpl only works when output-folder starts with ./
#142
mbenary
closed
2 years ago
0
New routine: `sodar check-remote` (#135)
#141
Nicolai-vKuegelgen
closed
2 years ago
0
`snappy pull-processed-data`: accept list of file type as argument
#140
eudesbarbosa
opened
2 years ago
0
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