galaxyproject/foundry

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The Galaxy Workflow Knowledge Base

Stars: 2
Forks: 3
Open beginner issues: 9
Indexed issues: 80
Avg merge: 19h 23m
Merged PRs (30d): 60

Dominant language: TypeScript
License: No license data
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 16, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

Augment freeform-to-Workflow Brief scenarios with real source artifacts Open

needs-triage

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

galaxyproject/foundry#592 · Opened Sep 20, 2026
`download?style=ga` emits unversioned `tool_id`s, producing workflows that save but cannot be invoked Open

needs-triage

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

galaxyproject/foundry#591 · Opened Sep 18, 2026
Authoring never checks a wrapped script's own declared input-ordering assumption against the tool it will consume from Open

needs-triage

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

galaxyproject/foundry#590 · Opened Sep 18, 2026
`PUT /api/workflows/{id}` defaults `exact_tools` to true and discards the per-step detail it already computed Open

needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 68/100

galaxyproject/foundry#589 · Opened Sep 18, 2026
A `sample_sheet` column was wired onto a plain scalar tool port, a binding that can never work Open

needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 52/100

galaxyproject/foundry#588 · Opened Sep 18, 2026
gxformat2 has no `tool_uuid`, so a step bound to a registered UDT imports unresolved Open

needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 55/100

galaxyproject/foundry#587 · Opened Sep 18, 2026
Galaxy's unprivileged-tool lint fails opaquely on an integer input with `value: 0` Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 68/100

galaxyproject/foundry#586 · Opened Sep 18, 2026
The real UDT registration endpoint is `/api/unprivileged_tools`, not the admin-only `/api/dynamic_tools` Open

needs-triage

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

galaxyproject/foundry#585 · Opened Sep 18, 2026
Invocation-failure reference has no tell for a stale toolbox read vs. a real install failure Open

needs-triage

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

galaxyproject/foundry#584 · Opened Sep 18, 2026
`replacement_collection` indexes `rows` unconditionally, crashing Planemo staging for a `sample_sheet` input without `rows` Open

needs-triage

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

galaxyproject/foundry#583 · Opened Sep 18, 2026
No documented path for an authored `GalaxyUserTool` to reach a Planemo-managed toolbox Open

needs-triage

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

galaxyproject/foundry#582 · Opened Sep 18, 2026
`gxwf validate --connections` crashes on an ordinary format2 dict-shaped `step.in` Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 72/100

galaxyproject/foundry#581 · Opened Sep 18, 2026
`comments: type: frame` authored without `position`/`size` is rejected by real Galaxy import Open

needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 56/100

galaxyproject/foundry#580 · Opened Sep 18, 2026
No packaged note documents the `sample_sheet` + `rows:` job-input shape Open

needs-triage

Difficulty 1/5 1-3 hours Newbie friendliness 88/100

galaxyproject/foundry#579 · Opened Sep 18, 2026
tests-format has no way to put a value on an intermediate step's input port Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 66/100

galaxyproject/foundry#578 · Opened Sep 18, 2026
`freeform-summary-to-galaxy-test-plan` is silent on being handed a concrete draft and resolved test-data refs Open

needs-triage

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

galaxyproject/foundry#577 · Opened Sep 18, 2026
Test-plan schema requires a file-shaped `fixture` for plain scalar workflow parameters Open

needs-triage

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

galaxyproject/foundry#576 · Opened Sep 18, 2026
`paper-to-test-data` has no scoping or upstream-fixture guidance, and is the weaker half of its own fallback chain Open

needs-triage

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

galaxyproject/foundry#575 · Opened Sep 18, 2026
`gxwf tool-search` returns zero hits for a literal Tool Shed repo slug Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 68/100

galaxyproject/foundry#574 · Opened Sep 18, 2026
`implement-galaxy-tool-step` documents no binding convention for an authored UDT Open

needs-triage

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

galaxyproject/foundry#573 · Opened Sep 18, 2026
ToolShed-fetch decoder rejects a real IUC wrapper's filtered list-collection output Open

needs-triage

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

galaxyproject/foundry#572 · Opened Sep 18, 2026
`gxformat2-schema` documents nested `state` but not nested `in:` key addressing Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 72/100

galaxyproject/foundry#571 · Opened Sep 18, 2026
Pattern MOCs are cast without the pattern pages they point at Open

needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 55/100

galaxyproject/foundry#570 · Opened Sep 18, 2026
Review New Paper Open

agent/implement priority/mvp roadmap/off

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

galaxyproject/foundry#568 · Opened Sep 18, 2026
Needs better guidance for importing to a real galaxy instance Open

needs-triage

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

galaxyproject/foundry#566 · 2 comments · Opened Sep 17, 2026
advance-galaxy-draft-step/repair-galaxy-draft-topology can produce step doc: text long enough to crash workflow import on live Galaxy instances; no lint/validate check catches it Open

needs-triage

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

galaxyproject/foundry#564 · 2 comments · Opened Sep 17, 2026
Workflow Plan Open

needs-triage

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

galaxyproject/foundry#563 · 1 comment · Opened Sep 17, 2026
Sandbox Support - agent-safehouse Open

needs-triage

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

galaxyproject/foundry#562 · Opened Sep 17, 2026
No reachable route serves a Tool Shed wrapper's raw XML at a pinned changeset Open

enhancement needs-triage

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

galaxyproject/foundry#553 · 1 comment · Opened Sep 16, 2026
advance-galaxy-draft-step's built-in/stock version branch is circular Open

bug needs-triage

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

galaxyproject/foundry#552 · Opened Sep 16, 2026
`gxwf draft-validate --concrete`: the other half of #166 — a ParsedTool decode failure's `Error.message` is still a full type declaration Open

bug needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 55/100

galaxyproject/foundry#548 · 2 comments · Opened Sep 16, 2026
Profiling the per-step draft loop: it is model-bound, not network-bound Open

documentation needs-triage

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

galaxyproject/foundry#547 · Opened Sep 16, 2026
Prove the IWC review pipeline on a real PR and accept its policy pin Open

agent/implement enhancement priority/mvp roadmap/main

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

galaxyproject/foundry#535 · Opened Sep 15, 2026
Replace abstract summarize-nextflow scenarios with concrete pinned fixtures Open

agent/implement needs-triage

Difficulty 4/5 3-5 days Newbie friendliness 68/100

galaxyproject/foundry#534 · Opened Sep 15, 2026
Prove the IWC maturation pipeline with runnable fixtures and a .ga entry case Open

agent/implement enhancement priority/mvp roadmap/main

Difficulty 4/5 3-5 days Newbie friendliness 50/100

galaxyproject/foundry#531 · Opened Sep 15, 2026
Improved Structure and Schemas for Mold Artifacts Open

priority/v2 roadmap/main

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

galaxyproject/foundry#507 · Opened Sep 12, 2026
Ensure every pattern page has a test workflow. Open

priority/mvp roadmap/substep

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

galaxyproject/foundry#505 · Opened Sep 12, 2026
Improve Pattern Pages Open

enhancement priority/mvp roadmap/main

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

galaxyproject/foundry#504 · Opened Sep 12, 2026
Improved Support for Tool Development Open

priority/mvp roadmap/main

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

galaxyproject/foundry#501 · Opened Sep 12, 2026
Implement actual interviews. Open

priority/mvp roadmap/main

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

galaxyproject/foundry#500 · Opened Sep 12, 2026
First Class CWL Support Open

priority/v2 roadmap/main

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

galaxyproject/foundry#499 · Opened Sep 12, 2026
Build a Pi-backed black-box Pipeline evaluation harness Open

priority/mvp roadmap/main

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

galaxyproject/foundry#476 · Opened Aug 28, 2026
author-galaxy-tool-wrapper: no validation step, no GalaxyUserTool schema, and the bundled prompt contradicts it Open

agent/implement priority/mvp roadmap/substep

Difficulty 4/5 3-5 days Newbie friendliness 68/100

galaxyproject/foundry#468 · 1 comment · Opened Aug 19, 2026
paper-to-cwl: a missing cwl-test-plan producer, and find-test-data used off its target axis Open

priority/v2 roadmap/substep

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

galaxyproject/foundry#448 · Opened Aug 5, 2026
The Foundry Diagram Makes it look like Molds are not part of the KB Open

bug priority/v2 roadmap/off

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

galaxyproject/foundry#415 · Opened Jul 30, 2026
First walk: cwl-to-galaxy end-to-end via ga4gh_challenge (earn the CWL-source tier out of draft) Open

enhancement priority/v2 roadmap/substep

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

galaxyproject/foundry#378 · Opened Jul 24, 2026
interview-to-freeform-summary is reviewed + pipelined but declares zero references Open

priority/mvp roadmap/substep

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

galaxyproject/foundry#377 · Opened Jul 24, 2026
Include upstream advice/prompts/docs for tool development. Open

enhancement priority/mvp roadmap/substep

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

galaxyproject/foundry#368 · 3 comments · Opened Jul 22, 2026
Foundry should use (or know about) job cache Open

enhancement priority/mvp roadmap/main

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

galaxyproject/foundry#365 · 1 comment · 1 reaction · Opened Jul 21, 2026
Introduce a finalize-workflow step. Open

enhancement priority/mvp roadmap/main

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

galaxyproject/foundry#332 · Opened Jun 19, 2026

galaxyproject/foundry

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