القائمة
Router skill for Nextflow to Galaxy conversions - directs to appropriate sub-skill
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Use when authoring a Galaxy User-Defined Tool (UDT) -- a `class: GalaxyUserTool` YAML definition that wraps a container and command into a tool a non-admin user creates and runs (e.g. via Galaxy MCP create_user_tool / run_user_tool, or POST /api/unprivileged_tools). Not for classic XML/ToolShed tool wrappers.
Use this skill when asked to create, draft, or write a Galaxy workflow report template for the Workflow Editor's Report tab. Triggers on requests like "create a report for this workflow", "draft a workflow report template", "write a Galaxy report for workflow <id/url>".
Galaxy Collection Transformation Command - transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest, merge, or otherwise manipulate Galaxy collections.
Galaxy MCP server tools reference for histories, datasets, tools, and workflows
Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation
Building UCSC Track Hubs (track hubs and assembly hubs) — bigBed/bigChain/bigMaf format requirements, composite-track rules, hub.txt / genomes.txt / trackDb.txt structure. Use when emitting a UCSC hub from Galaxy outputs, wrapping a hub-publishing tool, or debugging hubCheck failures.
| name | nf-to-galaxy |
| description | Router skill for Nextflow to Galaxy conversions - directs to appropriate sub-skill |
This is a router skill that directs you to the appropriate specialized skill based on what you're converting.
For complete pipelines, you are expected to include bioinformatics best-practice sanity checks and discuss QC + reporting requirements (e.g. MultiQC). See nf-pipeline-to-galaxy-workflow/SKILL.md.
Converting: One Nextflow process to one Galaxy tool XML
Example: HYPHY_FEL process → hyphy_fel.xml tool
Use skill: nf-process-to-galaxy-tool
When to use:
Converting: Multiple connected Nextflow processes to a Galaxy workflow
Example: PROCESS_VIRAL_NONRECOMBINANT subworkflow → Galaxy .ga workflow
Use skill: nf-subworkflow-to-galaxy-workflow
When to use:
Converting: Full Nextflow pipeline to complete Galaxy solution
Example: CAPHEINE pipeline → Multiple Galaxy workflows + any missing tools
Use skill: nf-pipeline-to-galaxy-workflow
When to use:
Before using any sub-skill, understand these mappings:
| Aspect | Nextflow | Galaxy |
|---|---|---|
| Unit of work | Process (Groovy DSL) | Tool (XML) |
| Organization | Module (directory) | Tool directory |
| Workflow format | .nf files (code) | .ga files (JSON) |
| Dependencies | Containers or Conda | Conda via <requirements> |
| Inputs/Outputs | Channels | Datasets with datatypes |
Critical: One Nextflow process = One Galaxy tool
Read: nextflow-galaxy-terminology.md for detailed conceptual mapping
New to this skill? See README.md for file organization and navigation.
Using Galaxy integration? See ../../galaxy-integration/README.md and ../../galaxy-integration/galaxy-integration.md.
../../galaxy-integration/galaxy-integration.md - Galaxy MCP/BioBlend: setup, tool checking, workflow testingcheck-tool-availability.md - Manual tool checking across repositoriestesting-and-validation.md - Routing page to canonical testing docs../../tool-dev/references/testing.md - Tool testing with PlanemoBefore you conclude a tool is "missing", distinguish:
.ga).If you determine (3) applies, use nf-process-to-galaxy-tool/ to create a Galaxy tool wrapper.
When a tool is not installed on the target instance, follow the repository search order in check-tool-availability.md.
Common ToolShed owners to check (not exhaustive):
iucdevteambgrueninggenouestnextflow-galaxy-terminology.md - Concept mappings (process→tool, workflow→.ga)process-to-tool.md - Process → Tool conversion detailsworkflow-to-ga.md - Workflow → .ga conversion detailscontainer-mapping.md - Container → Conda package mappingdatatype-mapping.md - File patterns → Galaxy datatypestool-sources.md - Where to create tools (tools-iuc vs custom)scripts/ - Automation scripts (see scripts/README.md)examples/ - Complete conversion examples (see examples/README.md)What are you converting?
│
├─ Single process?
│ └─ Use: nf-process-to-galaxy-tool
│
├─ Subworkflow (multiple processes)?
│ └─ Use: nf-subworkflow-to-galaxy-workflow
│
└─ Complete pipeline?
└─ Use: nf-pipeline-to-galaxy-workflow
nf-process-to-galaxy-tool/Convert a single Nextflow process to a Galaxy tool XML.
nf-subworkflow-to-galaxy-workflow/Convert a Nextflow subworkflow to a Galaxy workflow.
nf-pipeline-to-galaxy-workflow/Convert a complete Nextflow pipeline to a Galaxy solution.