Owner

pepkit

8 indexed repositories · View on GitHub

pephub
A web API and database for biological sample metadata

TypeScript · 22 stars
pepspec
Documentation for PEP specification and all PEPkit software

Python · 10 stars
eido
Validator for PEP objects

Python · 5 stars
pepr
Project metadata manager for PEPs in R

R · 3 stars
pephubclient
A tool to provide Python and CLI interface and Python API for PEPhub.

Python · 3 stars
peprs
PEP implementation in memory safe language Rust

Rust · 3 stars
pepdbagent
Database for storing sample metadata

Python · 2 stars
pepembed
Indexer of pephub database

Python · 1 star

Beginner friendly Everything

Open All

Validation of huge (>10K samples) projects Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

pepkit/pephub#460 · Opened Jul 6, 2026
When building from `SampleYAML`, the sample index column is not cast to `DataType::String` [potential BUG] Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

pepkit/peprs#44 · Opened Apr 18, 2026
Fix python publisher warning Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

pepkit/peprs#42 · Opened Apr 5, 2026
Missing features from peprs Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

pepkit/peprs#33 · Opened Mar 24, 2026
Add function `add_sample` that adds sample to the project Open

brainstorming

Difficulty 3/5 1-2 days Newbie friendliness 55/100

pepkit/peprs#32 · Opened Mar 23, 2026
Investigate if wdl works with peprs Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

pepkit/peprs#24 · Opened Mar 10, 2026
Implement a `from_pephub` method Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

pepkit/peprs#17 · 4 comments · Opened Oct 14, 2025
Goal: integrate `peprs` into PEPATAC and other packages Open

integration

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/peprs#14 · 1 comment · Opened Oct 13, 2025
Figure out sample merging Open

wontfix

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/peprs#11 · 1 comment · Opened Oct 13, 2025
The README is hard to follow for deploying PEPhub locally Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

pepkit/pephub#445 · 6 comments · Opened Oct 3, 2025
Better authentication Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

pepkit/pephub#444 · 1 comment · Opened Sep 26, 2025
Add ability to pass pephub API key when creating phc object Open

enhancement question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pephubclient#54 · Opened Sep 25, 2025
Consider Publishing Pepr to a Conda repo for Snakemake Integration Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

pepkit/pepr#49 · 1 comment · Opened Jul 29, 2025
Ordering PEP csv by colunn Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

pepkit/pephub#443 · Opened Jul 10, 2025
Properly handle relative paths for schema imports Open

likely-solved

Difficulty 3/5 1-2 days Newbie friendliness 48/100

pepkit/eido#81 · Opened Jun 5, 2025
Renaming PEP does not show up in history of changes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

pepkit/pephub#442 · 1 reaction · Opened May 22, 2025
Forking PEP sometimes gives unknown error Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

pepkit/pephub#441 · Opened May 21, 2025
Make archiving automatic Open

priority high

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/pephub#440 · Opened May 21, 2025
derived sample_names cannot be modified Open

bug server-side

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pephub#439 · Opened May 20, 2025
schemas should be sorted by date, rather than alphabetically Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pepkit/pephub#437 · Opened May 20, 2025
Update geo archive loading text Open

Difficulty 1/5 Under an hour Newbie friendliness 45/100

pepkit/pephub#435 · Opened Apr 29, 2025
History is not updated when pushing results to PEPhub via pephubclient Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

pepkit/pephubclient#53 · Opened Apr 21, 2025
Sometimes results are not reported back to pephub using pipestat and phc Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

pepkit/pephubclient#52 · Opened Apr 18, 2025
Visual bug with table and `0` values Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pepkit/pephub#433 · 1 comment · Opened Apr 18, 2025
Add privacy to the schemas Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pephub#430 · Opened Mar 31, 2025
Forking schemas Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/pephub#429 · Opened Mar 31, 2025
schema submission demo Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pepkit/pephub#424 · Opened Mar 25, 2025
More Sample Table Issues Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pephub#416 · 3 comments · Opened Mar 11, 2025
PEPhub wont save my PEP Open

bug help wanted

Difficulty 3/5 1-2 days Newbie friendliness 48/100

pepkit/pephub#414 · 2 comments · Opened Jan 27, 2025
Eido fails to recognize integer type in PEP Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pepkit/eido#80 · Opened Jan 26, 2025
Proper handling of empty attribute when minLength=1 Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

pepkit/eido#79 · 1 comment · Opened Dec 23, 2024
Cancel button should cancel OR be called something else Close Open

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

pepkit/pephub#413 · 1 comment · Opened Dec 10, 2024
Performance with background tasks Open

brainstorming

Difficulty 4/5 3-5 days Newbie friendliness 25/100

pepkit/pephub#396 · Opened Sep 20, 2024
Great opportunity to use `@tanstack/react-table`... really a fantastic library Open

UI/UX

Difficulty 5/5 Over a week Newbie friendliness 20/100

pepkit/pephub#390 · Opened Sep 18, 2024
Add archiving of schemas Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/pephub#386 · Opened Sep 10, 2024
Evaluate JWT at the correct time Open

priority low

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pephub#385 · Opened Sep 3, 2024
Views have a weird relationship with handsontable views Open

priority low

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/pephub#382 · Opened Aug 30, 2024
Project name shouldn't be inside the project Open

priority low

Difficulty 5/5 Over a week Newbie friendliness 25/100

pepkit/pephub#381 · Opened Aug 30, 2024
Fix mobile views Open

priority low UI/UX

pepkit/pephub#378 · 1 assignee · Opened Aug 28, 2024
How do we convert the `handsontable` sample table representation to a PEP-compatible sample table representation? Open

likely solved

pepkit/pephub#376 · 3 comments · 1 assignee · Opened Aug 22, 2024
PEPhubclient should correctly handle domains for registry paths Open

bug

pepkit/pephubclient#48 · 5 comments · 1 assignee · Opened Aug 22, 2024
Please improve the error message if I provide a bad registry path Open

pepkit/pephubclient#46 · 1 assignee · Opened Aug 22, 2024
Mechanism for collecting feedback Open

likely solved

Difficulty 5/5 Over a week Newbie friendliness 35/100

pepkit/pephub#371 · 4 comments · Opened Aug 14, 2024
Improving the views interface Open

enhancement UI/UX

pepkit/pephub#370 · 2 comments · 1 assignee · Opened Aug 14, 2024
History interface should have a 'fork' or tag button Open

priority low UI/UX

Difficulty 3/5 1-2 days Newbie friendliness 42/100

pepkit/pephub#367 · 1 comment · Opened Aug 14, 2024
Can we make the `ph_id` column read only? Open

wontfix

Difficulty 3/5 1-2 days Newbie friendliness 30/100

pepkit/pephub#364 · 1 comment · Opened Jul 30, 2024
Add docs about schema and validation Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 25/100

pepkit/pephub#363 · Opened Jul 25, 2024
UI checklist for next update Open

likely solved UI/UX

pepkit/pephub#361 · 1 assignee · Opened Jul 25, 2024
Add indexes in sqlalchemy models Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

pepkit/pepdbagent#141 · Opened Jul 8, 2024
Fail nicely if jwt is incorrect Open

good first issue

Difficulty 3/5 1-2 days Newbie friendliness 45/100

pepkit/pephubclient#42 · Opened Jul 2, 2024

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