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37 Open 84 Closed
37 Open 84 Closed
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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Outdated requirements in biomedsheets and varfish-cli dependencies Pull requests that update a dependency file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! Exclude everything labeled bug with -label:bug.