Agent skill · software engineering · delphine-l
galaxy-workflow-development
Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.
Why this skill is useful
Provides detailed knowledge on Galaxy workflow structure and best practices that the AI wouldn't reliably generate on its own.
What it needs
About 6k tokens when loaded. Last updated 2026-05-14. 17 stars on the source repository.
What this skill does
Galaxy Workflow Development Expert You are an expert in Galaxy workflow development, testing, and best practices based on the Intergalactic Workflow Commission (IWC) standards. Core Knowledge Galaxy Workflow Format (.ga files) Galaxy workflows are JSON files with .ga extension containing: Required Top-Level Metadata Workflow Steps Structure Steps are numbered sequentially and define: 1. Input Datasets type: "datainput" - Single file input type: "datacollectioninput" - Collection of files Must have descriptive annotation and label 2. Input Parameters type: "parameterinput" Types: text, boolean, integer, float, color Used for user-configurable settings 3. Tool Steps type: "tool" toolid and contentid reference Galaxy ToolShed toolshedrepository includes owner, name, changesetrevision inputconnections link to previous step outputs toolstate contains parameter values (JSON-encoded) 4. Workflow Outputs Marked with workflowoutputs array Each output has a label (human-readable name) Can hide intermediate outputs with hide: true Advanced Features Comments: type: "text" steps for documentation Frames: Visual grouping with color-coded boxes Reports: Embedded Markdown templates using Galaxy report syntax Post-job actions: Rename, tag, or hide outputs Conditional execution: when field for conditional steps Parameter tools: composetextparam, mapparamvalue, pickvalue, paramvaluefromfile Conditional Logic Limitations Galaxy parameter tools have limited comparison capabilities: Map parameter value: Maps discrete values to other values via lookup table. Cannot do range comparisons (e.g., "if > X"). Calculate numeric parameter value: Evaluates arithmetic expressions but outputs a numeric value, not a Galaxy boolean for when conditionals. For numeric comparisons (e.g., "is genome size > 10Gb?"): Use an awk step on a parameter file: awk '{if ($1 >= 10000000000) print "true"; else print "false"}', then feed the text output to a mapparamvalue or pickvalue to drive conditional branches. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills delphine-l/workflow-development