galaxyproject/foundry

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The Galaxy Workflow Knowledge Base

Stars: 2
Forks: 3
Open beginner issues: 0
Indexed issues: 48
Avg merge: 1d 22m
Merged PRs (30d): 63

Dominant language: TypeScript
License: No license data
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 16, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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47 open issues indexed

Hero pipeline-fan widget (replace pipeline matrix / new /pipelines/ landing) Open

agent/implement priority/v2 roadmap/off

galaxyproject/foundry#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Write IWC exemplar match schema Open

agent/implement priority/v2 roadmap/main

galaxyproject/foundry#40 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Write target test plan schema Open

agent/research enhancement priority/v2 roadmap/substep

galaxyproject/foundry#48 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Write workflow test run report schema Open

agent/research enhancement priority/v2 roadmap/substep

galaxyproject/foundry#49 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Write workflow debug recommendation schema Open

agent/research enhancement priority/v2 roadmap/substep

galaxyproject/foundry#50 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Research Nextflow process to Galaxy tool wrapper mapping Open

priority/mvp roadmap/main

galaxyproject/foundry#59 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Research Nextflow test fixtures to Galaxy job inputs Open

priority/mvp roadmap/main

galaxyproject/foundry#66 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Survey: Galaxy reporting and publishing patterns Open

priority/mvp roadmap/main

galaxyproject/foundry#90 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Set legacy DSL1 support posture for Nextflow file and set pipelines Open

priority/v2 roadmap/off

galaxyproject/foundry#176 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Evaluate Galaxy pattern for Nextflow workflow output index files Open

agent/research priority/v2 roadmap/off

galaxyproject/foundry#175 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Galaxy sample-sheet column-value charset gate rejects nf-core canonical values Open

priority/v2 roadmap/off upstream/galaxy

galaxyproject/foundry#191 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
summarize-nextflow: resolve from_param through one-hop Groovy bindings Open

agent/implement priority/v2 roadmap/off

galaxyproject/foundry#211 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
summarize-nextflow: derived subworkflow-level edge view Open

agent/implement priority/v2 roadmap/off

galaxyproject/foundry#215 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
summarize-nextflow: parsed predicate sibling on conditionals[].guard (_derived_pattern) Open

agent/implement priority/v2 roadmap/off

galaxyproject/foundry#216 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
research: flesh out nextflow-to-galaxy-reference-data-mapping Open

priority/mvp roadmap/off

galaxyproject/foundry#219 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
research: ref-data complexity bridge fixtures for nextflow-to-galaxy mapping Open

agent/research priority/v2 roadmap/off

galaxyproject/foundry#221 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Document Galaxy list-of-record collections for reference data Open

enhancement priority/v2 roadmap/main upstream/galaxy

galaxyproject/foundry#225 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
summarize-cwl: tighten cast skill's deterministic/LLM split Open

enhancement priority/v2 roadmap/substep

galaxyproject/foundry#231 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
summarize-cwl: emit a skinny packed CWL (docs + schema.org stripped) alongside the full pack Open

agent/implement priority/v2 roadmap/substep

galaxyproject/foundry#243 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add docs/README.md — human reading order / docs index Open

agent/implement documentation priority/v2 roadmap/off

galaxyproject/foundry#246 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Surface the _provenance.json schema v2 as a renderable schema reference Open

agent/implement documentation priority/v2 roadmap/off

galaxyproject/foundry#252 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Generated STATUS page — what exists, last-touched (fun, not urgent) Open

agent/implement documentation enhancement priority/v2 roadmap/off

galaxyproject/foundry#254 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Source-agnostic Galaxy input collection-shape selection note (+ IWC survey to ground it) Open

enhancement priority/mvp roadmap/main

galaxyproject/foundry#267 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Decide gops_* vs bedtools interval-tool redundancy (interval MOC) Open

agent/research priority/v2 requires-iwc-inputs roadmap/off

galaxyproject/foundry#271 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Galaxy pipeline Molds write fixed filenames to cwd — namespace per-source run Open

bug priority/v2 roadmap/off

galaxyproject/foundry#282 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Data Flow Examples on Multi-Step Patterns Open

priority/v2 roadmap/substep

galaxyproject/foundry#284 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Pipeline construction for Loom/Orbit: a `loom` cast target that lowers pipelines into Loom plans Open

priority/mvp roadmap/main

galaxyproject/foundry#306 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Design a Claude dynamic-workflow projection for Foundry Pipelines Open

agent/research priority/v2 roadmap/main

galaxyproject/foundry#308 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Revise how skills working on draft coordinate - more direct, more deterministic, more YAML Open

enhancement priority/mvp roadmap/main

galaxyproject/foundry#318 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Introduce a finalize-workflow step. Open

enhancement priority/mvp roadmap/main

galaxyproject/foundry#332 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Foundry should use (or know about) job cache Open

enhancement priority/mvp roadmap/main

galaxyproject/foundry#365 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Include upstream advice/prompts/docs for tool development. Open

enhancement priority/mvp roadmap/substep

galaxyproject/foundry#368 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
interview-to-freeform-summary is reviewed + pipelined but declares zero references Open

priority/mvp roadmap/substep

galaxyproject/foundry#377 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 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

galaxyproject/foundry#378 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
The Foundry Diagram Makes it look like Molds are not part of the KB Open

bug priority/v2 roadmap/off

galaxyproject/foundry#415 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
paper-to-cwl: a missing cwl-test-plan producer, and find-test-data used off its target axis Open

priority/v2 roadmap/substep

galaxyproject/foundry#448 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
author-galaxy-tool-wrapper: no validation step, no GalaxyUserTool schema, and the bundled prompt contradicts it Open

agent/implement priority/mvp roadmap/substep

galaxyproject/foundry#468 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Build a Pi-backed black-box Pipeline evaluation harness Open

priority/mvp roadmap/main

galaxyproject/foundry#476 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
First Class CWL Support Open

priority/v2 roadmap/main

galaxyproject/foundry#499 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Implement actual interviews. Open

priority/mvp roadmap/main

galaxyproject/foundry#500 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Improved Support for Tool Development Open

priority/mvp roadmap/main

galaxyproject/foundry#501 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Improve Pattern Pages Open

enhancement priority/mvp roadmap/main

galaxyproject/foundry#504 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Ensure every pattern page has a test workflow. Open

priority/mvp roadmap/substep

galaxyproject/foundry#505 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Improved Structure and Schemas for Mold Artifacts Open

priority/v2 roadmap/main

galaxyproject/foundry#507 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Prove the IWC maturation pipeline with runnable fixtures and a .ga entry case Open

agent/implement enhancement priority/mvp roadmap/main

galaxyproject/foundry#531 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Replace abstract summarize-nextflow scenarios with concrete pinned fixtures Open

agent/implement

galaxyproject/foundry#534 · 0 comments · 0 reactions · 0 assignees · Indexed 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

galaxyproject/foundry#535 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

galaxyproject/foundry

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