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automatic iinit in interactive mode broken

Status: Open.

#311 In bihealth/cubi-tk;

· stolpeo opened on Sep 29, 2025

snappy pull-raw-data subcommand does not find all fastq files

Status: Open.

#306 In bihealth/cubi-tk;

· ericblanc20 opened on Sep 23, 2025

Refactor to SodarPullBase

Status: Open.

#304 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Sep 23, 2025

Add functionality to delete lz or files from lzs

Status: Open.

#299 In bihealth/cubi-tk;

· slaemmle opened on Sep 9, 2025

Creating a bulk RNA-Seq ISA template fails

Status: Open.

#291 In bihealth/cubi-tk;

· january3 opened on Jul 9, 2025

Fully deprecate <code>cubi_tk/irods/check.py</code>

Status: Open.

#280 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Apr 28, 2025

<code>cubi-tk sodar add-ped</code> does not write metadata to index when used to update existing entires

Status: Open.

#269 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Feb 26, 2025

<code>cubi-tk sodar update samplesheet</code> autofill does not work correctly on small/template projects

Status: Open.

#268 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Feb 26, 2025

<code>cubi-tk sodar add-ped</code> expects the <code>Library Name</code> Column to exist

Status: Open.

#267 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Feb 26, 2025

Add file type filters to <code>cubi-tk sodar check-remote</code> and allow optional output suppression

Status: Open.

#230 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Apr 10, 2024

The <code>parse_irods_collection</code> function filters out md5 files

Status: Open.

#229 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Apr 10, 2024

<code>cubi-tk snappy pull-raw-data --dry-run</code> only reports fastq files that match the library name

Status: Open.

#194 In bihealth/cubi-tk;

· Nicolai-vKuegelgen opened on Sep 19, 2023