Skip to content

Issues: bihealth/cubi-tk

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

37 Open 84 Closed
37 Open 84 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Update cubi-tk dependencies and build process
#238 opened Aug 19, 2024 by Nicolai-vKuegelgen
4 tasks
@tedil
Not all landing zones listed with cubi-tk sodar list-landingzones
#234 opened Aug 15, 2024 by your-highness
1
Add file type filters to cubi-tk sodar check-remote and allow optional output suppression
#230 opened Apr 10, 2024 by Nicolai-vKuegelgen
The parse_irods_collection function filters out md5 files
#229 opened Apr 10, 2024 by Nicolai-vKuegelgen
cubi-tk snappy itransfer-* LZ selection is faulty
#209 opened Jan 17, 2024 by Nicolai-vKuegelgen
Refactor commonly use functionality, esp. from cubi-tk snappy
#201 opened Nov 7, 2023 by Nicolai-vKuegelgen
2
1
cubi-tk snappy pull-raw-data --dry-run only reports fastq files that match the library name
#194 opened Sep 19, 2023 by Nicolai-vKuegelgen
Update defaults for snappy itransfer-* tools
#191 opened Sep 7, 2023 by Nicolai-vKuegelgen
1
Should irods check validate the stored data or against the md5 file question Further information is requested
#185 opened Jun 30, 2023 by xiamaz
4
Integrate snappy pull-data into workflow configuration enhancement New feature or request
#183 opened Jun 15, 2023 by xiamaz
Do not require a pipeline-job.sh for each pipeline step when using snappy kickoff
#177 opened Jun 7, 2023 by xiamaz
Replace logzero as logging solution
#172 opened May 19, 2023 by sellth
1
cubi-tk snappy pull-sheets has undocumented samplehseet requirements
#164 opened Apr 24, 2023 by Nicolai-vKuegelgen
2
snappy pull-processed-data: accept list of file type as argument
#140 opened Nov 10, 2022 by eudesbarbosa
Add more itransfer commands
#121 opened Sep 12, 2022 by holtgrewe
1
Error while parsing optional columns in snappy pull-sheets
#120 opened Sep 9, 2022 by eudesbarbosa
Mislabeled "sample names" in ISA-Tab templates
#106 opened Jun 30, 2022 by mikkonie
1
@sellth
Outdated requirements in biomedsheets and varfish-cli dependencies Pull requests that update a dependency file
#90 opened Apr 7, 2022 by mikkonie
@mikkonie
1
varfish-upload: allow empty SV files
#88 opened Mar 11, 2022 by eudesbarbosa
Duplicate sequencing
#62 opened Jul 15, 2021 by ericblanc20
@holtgrewe @mbenary
@ericblanc20 @eudesbarbosa
2
Unit test pull_sheets.SampleSheetBuilder
#50 opened Jun 28, 2021 by eudesbarbosa
Add cubi-tk snappy zap-output enhancement New feature or request
#45 opened Jun 14, 2021 by holtgrewe
The itransfer commands fail if not called from the correct path
#32 opened Feb 19, 2021 by holtgrewe
Make iRODS-related commands check whether the user is logged in first
#30 opened Feb 19, 2021 by holtgrewe
Provide a way to install without pandas
#27 opened Feb 12, 2021 by holtgrewe
1
ProTip! no:milestone will show everything without a milestone.