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bihealth
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cubi-tk
CUBI Tooling for SODAR, VarFish et al.
MIT License
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feat: add `--filter-status` option for controlling which landing zones are listed
#239
tedil
opened
2 months ago
2
Update cubi-tk dependencies and build process
#238
Nicolai-vKuegelgen
opened
3 months ago
0
chore: pin snappy version to v0.1.1 in requirements.txt
#237
tedil
closed
3 months ago
0
CI workflow fails with newest snappy version
#236
Nicolai-vKuegelgen
closed
3 months ago
3
feat: presets for cubi-tk sodar ingest-fastq (#232 )
#235
Nicolai-vKuegelgen
closed
2 months ago
1
Not all landing zones listed with `cubi-tk sodar list-landingzones`
#234
your-highness
opened
3 months ago
1
fix: isa-tab add-ped now only modifies values on process nodes of ped-supplied samples #207
#233
Nicolai-vKuegelgen
closed
5 months ago
0
Enhance `cubi-tk sodar ingest-fastq` with (regex) presets
#232
Nicolai-vKuegelgen
closed
2 months ago
0
fix: parsing snappy config for with WGS projects
#231
Nicolai-vKuegelgen
closed
7 months ago
1
Add file type filters to `cubi-tk sodar check-remote` and allow optional output suppression
#230
Nicolai-vKuegelgen
opened
7 months ago
0
The `parse_irods_collection` function filters out md5 files
#229
Nicolai-vKuegelgen
opened
7 months ago
0
chore(deps): bump black from 23.1.0 to 24.3.0 in /requirements
#228
dependabot[bot]
opened
8 months ago
0
feat: irods download refactoring and new generic sodar downloader with preset for dragen data (#226 )
#227
Nicolai-vKuegelgen
closed
7 months ago
2
New sodar downloader for Dragen data
#226
Nicolai-vKuegelgen
closed
7 months ago
0
fix: varfish-upload subprocess submission
#225
Nicolai-vKuegelgen
closed
9 months ago
1
feat: allow varfish case resubmission
#224
Nicolai-vKuegelgen
closed
9 months ago
2
ci: Remove versioneer; use release-please for versioning
#223
sellth
closed
5 months ago
1
fix: varfish cli 06x uses new import syntax (#220)
#222
Nicolai-vKuegelgen
closed
10 months ago
3
fix: adapt to varfish-cli >=0.6.2 syntax
#221
Nicolai-vKuegelgen
closed
10 months ago
1
varfish-cli >0.6.x uses new import syntax
#220
Nicolai-vKuegelgen
closed
10 months ago
2
feat: Add new command sodar landing-zone-validate
#219
sellth
closed
10 months ago
1
chore: Use Python 3.10+ context manager syntax
#218
sellth
closed
10 months ago
1
feat: Switching `cubi-tk sodar ingest-fastq` from icommands to irods_common
#217
Nicolai-vKuegelgen
closed
10 months ago
1
chore: bump minimal Python version to 3.10
#216
holtgrewe
closed
10 months ago
0
ci: Update Python versions we test against.
#215
sellth
opened
10 months ago
7
Newest varfish-cli is not compatible with python 3.8
#214
Nicolai-vKuegelgen
closed
3 months ago
2
feat: Adding cubi-tk snappy itransfer_sv_calling
#213
Nicolai-vKuegelgen
closed
10 months ago
1
Refactor `cubi-tk sodar ingest-fastq` to use iRODSTransfer
#212
Nicolai-vKuegelgen
closed
10 months ago
0
Need a `cubi-tk snappy itransfer-sv-calling` module
#211
Nicolai-vKuegelgen
closed
10 months ago
0
chore: Pin altamisa version; breaking changes incoming
#210
sellth
closed
10 months ago
1
`cubi-tk snappy itransfer-*` LZ selection is faulty
#209
Nicolai-vKuegelgen
opened
10 months ago
0
refactor: Use iRODSCommon as parent class
#208
sellth
opened
10 months ago
1
Bug: `cubi-tk (isa-tab|sodar) add-ped` is modifying previous Study Assay Data when `--library-kit` or `--library-kit-catalogue-id` is given
#207
your-highness
closed
5 months ago
3
feat: Add new command sodar landing-zone-validate
#206
your-highness
closed
10 months ago
2
Implement planned feature `sodar landing-zone-validate`
#205
your-highness
closed
10 months ago
0
chore: release 0.5.0
#204
github-actions[bot]
opened
1 year ago
0
feat: Update ingest-fastq, allow to match samples against assay table to determine collections names (#198)
#203
Nicolai-vKuegelgen
closed
1 year ago
4
feat: Common functions for interfacing with python-irodsclient
#202
sellth
closed
11 months ago
2
Refactor commonly use functionality, esp. from `cubi-tk snappy`
#201
Nicolai-vKuegelgen
opened
1 year ago
1
Switch from icommand usage to the python irods client
#200
Nicolai-vKuegelgen
closed
11 months ago
0
feat: Add generic SODAR ingest command
#199
sellth
closed
10 months ago
2
Allow ingest-fastq to match filenames to a specified column of the assay table
#198
Nicolai-vKuegelgen
closed
1 year ago
0
Need to adjust to varfish-cli changes
#197
holtgrewe
closed
3 months ago
1
chore: update build dependencies
#196
sellth
closed
1 year ago
1
fix: Update ISA-tpl dependencies
#195
sellth
closed
1 year ago
1
`cubi-tk snappy pull-raw-data --dry-run` only reports fastq files that match the library name
#194
Nicolai-vKuegelgen
opened
1 year ago
0
fix: Unpin Mamba version in CI workflow
#193
sellth
closed
1 year ago
1
refactor: Omit logger from coverage reports
#192
sellth
closed
1 year ago
1
Update defaults for snappy itransfer-* tools
#191
Nicolai-vKuegelgen
opened
1 year ago
1
Update to isa-tab not working when `i_Investigation.txt` is not in same subfolder as AssayData and SampleSheet
#190
your-highness
closed
11 months ago
12
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