galaxyproject/planemo

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Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.

Stars: 110
Forks: 102
Open beginner issues: 0
Indexed issues: 278
Avg merge: 4d 21h
Merged PRs (30d): 13

Dominant language: Python
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 16, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted

Beginner friendly Everything

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278 open issues indexed

Workflow test collection assertions are silently skipped unless spelled `element_tests` Open

Difficulty 3/5 1-2 days Newbie friendliness 76/100

galaxyproject/planemo#1705 · Opened Sep 14, 2026
workflow_lint --iwc does not check the date on the newest CHANGELOG heading Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

galaxyproject/planemo#1694 · Opened Sep 9, 2026
workflow_lint --iwc should error, not warn, when a workflow has no test cases Open

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

galaxyproject/planemo#1693 · Opened Sep 9, 2026
Run Engine for Embedded Galaxy Open

enhancement

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

galaxyproject/planemo#1686 · Opened Aug 25, 2026
Deduplicate planemo.io.wait_on in favor of galaxy.util.wait.wait_on Open

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

galaxyproject/planemo#1680 · Opened Aug 20, 2026
Meta: repository-level linting for data managers and tool data tables Open

enhancement linting

Difficulty 5/5 Over a week Newbie friendliness 28/100

galaxyproject/planemo#1672 · 2 comments · Opened Jul 24, 2026
planemo run --no_wait crashes with UnboundLocalError for tools Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

galaxyproject/planemo#1668 · Opened Jul 21, 2026
Global config values bypass click.Path conversion (resolve_path is dead code) Open

Difficulty 4/5 3-5 days Newbie friendliness 72/100

galaxyproject/planemo#1667 · Opened Jul 21, 2026
Add a GA4GH WES execution engine to `planemo run` (`--engine wes`) Open

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

galaxyproject/planemo#1651 · Opened Jun 6, 2026
Warning message when runing new planemo version Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

galaxyproject/planemo#1649 · Opened Jun 1, 2026
workflow_test_init fails with FileNotFoundError when workflow input labels contain forward slashes (/) Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

galaxyproject/planemo#1629 · Opened Mar 25, 2026
planemo test crashes when workflow test specifies non-existent outputs Open

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

galaxyproject/planemo#1625 · Opened Mar 5, 2026
Improve version linter Open

galaxyproject/planemo#1613 · 1 assignee · Opened Feb 9, 2026
Planemo improvements Open

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

galaxyproject/planemo#1602 · Opened Jan 27, 2026
Test functionality for ITs Open

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

galaxyproject/planemo#1600 · 3 reactions · Opened Jan 14, 2026
`planemo lint` false positive warning about `HelpInvalidRST` when using local images? Open

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

galaxyproject/planemo#1589 · 1 comment · Opened Dec 17, 2025
SyntaxWarning: Open

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

galaxyproject/planemo#1584 · Opened Nov 13, 2025
`--test_data` option of `planemo t` does not work Open

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

galaxyproject/planemo#1536 · Opened Jun 13, 2025
mulled-search gives error when searching GitHub sources due to lack of valid token Open

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

galaxyproject/planemo#1535 · Opened Jun 4, 2025
Getting ShedVersion error on unmodified tools that reside in the same directory that modified tools Open

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

galaxyproject/planemo#1525 · 1 comment · Opened May 12, 2025
workflow_test_init incorrect run from invocation Open

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

galaxyproject/planemo#1522 · 4 comments · Opened Apr 28, 2025
Add option to export a CLI-run to a galaxy instance Open

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

galaxyproject/planemo#1521 · 1 comment · Opened Apr 25, 2025
configure log level - decrease current output Open

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

galaxyproject/planemo#1516 · 1 comment · Opened Apr 15, 2025
Back up tool_test_output.* rather than overwriting Open

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

galaxyproject/planemo#1515 · Opened Apr 9, 2025
planemo run should work with dockstore id Open

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

galaxyproject/planemo#1508 · 1 reaction · Opened Mar 27, 2025
Default python version to loosely defined Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

galaxyproject/planemo#1489 · 2 comments · Opened Jan 27, 2025
CWL steps that return arrays of files should be discovered datasets Open

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

galaxyproject/planemo#1484 · 1 comment · Opened Dec 12, 2024
Enhancements for IWC Open

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

galaxyproject/planemo#1482 · 1 comment · Opened Nov 22, 2024
planemo autoupdate may fail on tools but exit code is 0 Open

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

galaxyproject/planemo#1478 · Opened Sep 26, 2024
planemo's configuration of bioblend's api key prevents running commands without authentication that don't require it Open

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

galaxyproject/planemo#1476 · 4 comments · Opened Sep 26, 2024
Synchronize with Galaxy Post 24.2 Publication Open

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

galaxyproject/planemo#1475 · 1 comment · Opened Sep 24, 2024
Return inputs ID in --test_output_json outputs Open

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

galaxyproject/planemo#1449 · Opened Apr 29, 2024
Allow initializing workflows from failed invocations Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

galaxyproject/planemo#1435 · Opened Mar 7, 2024
Output files detected with size 0 on planemo tests Open

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

galaxyproject/planemo#1431 · 2 comments · Opened Feb 10, 2024
Input staging problem: History not found Open

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

galaxyproject/planemo#1423 · Opened Jan 17, 2024
planemo lint workflow tests improvement Open

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

galaxyproject/planemo#1413 · Opened Dec 1, 2023
planemo lint multiple Open

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

galaxyproject/planemo#1411 · Opened Nov 20, 2023
Uploading/mirroring of test data Open

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

galaxyproject/planemo#1409 · 1 comment · Opened Nov 17, 2023
planemo autoupdate workflows improvements Open

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

galaxyproject/planemo#1404 · Opened Nov 13, 2023
planemo should catch when Python isn't there Open

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

galaxyproject/planemo#1392 · 1 comment · Opened Oct 6, 2023
planemo serve breaks with new docker version when running tools Open

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

galaxyproject/planemo#1390 · 5 comments · Opened Oct 3, 2023
Expose some history related option to test Open

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

galaxyproject/planemo#1380 · Opened Jul 27, 2023
planemo test is not recursive anymore Open

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

galaxyproject/planemo#1367 · 3 comments · Opened May 9, 2023
Symbolic links for tests data are not taken into account Open

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

galaxyproject/planemo#1366 · 1 comment · Opened May 9, 2023
[feature request] workflow_lint could use a structured data output Open

enhancement

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

galaxyproject/planemo#1360 · 1 comment · Opened Mar 24, 2023
Planemo test denies having updated test data Open

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

galaxyproject/planemo#1359 · Opened Mar 14, 2023
Add docker install requirement in the docs Open

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

galaxyproject/planemo#1354 · 3 comments · Opened Feb 16, 2023
`planemo test` parameter `--job_output_files` seems unused Open

galaxyproject/planemo#1352 · 1 comment · 1 assignee · Opened Feb 13, 2023
planemo serve does not display images in help section Open

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

galaxyproject/planemo#1349 · 1 reaction · Opened Jan 26, 2023
Rename the default branch to `main` Open

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

galaxyproject/planemo#1342 · Opened Dec 28, 2022

galaxyproject/planemo

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