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compare-against-iwc-exemplar

Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.

Mold health

Source layout
Directory Mold with only index.md frontmatter.
Axis fields
target-specific fields are coherent.
Eval plan
eval.md declares cases and check type.
Typed refs
6 typed references; 0 resolver issues.
On-demand triggers
All on-demand references describe triggers.
Evidence checks
Hypothesis references include verification.

axis: target-specific
target: galaxy
name: compare-against-iwc-exemplar

contract

Reference Loading

Typed Mold references describe what casting consumes and when the generated skill should load each artifact.

CLI Commandconvert

Command reference. Usually cast to a sidecar and loaded only when invoked.

Runtime On Demand Sidecar Corpus Observed

Purpose: Normalize fetched IWC workflows into a consistent representation for structural comparison.
Trigger: After fetching a candidate IWC workflow file and before structural comparison.

Researchgalaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Hypothesis

Purpose: Compare against the design briefs' abstract intent without turning exemplar comparison into tool resolution.
Trigger: When deciding whether to compare abstract data-flow shape, interface structure, or speculative implementation details.
Verify: Promote after exemplar comparison flags structural issues without resolving concrete tool metadata.

Patterngalaxy-collection-patterns

Workflow-construction idiom. Usually condensed during casting.

Runtime On Demand Verbatim Corpus Observed

Purpose: Compare proposed collection transformations against curated corpus-observed pattern guidance.
Trigger: When the data-flow brief proposes collection reshape, cleanup, relabel, synchronization, or collection-tabular bridge sections.

Patterngalaxy-tabular-patterns

Workflow-construction idiom. Usually condensed during casting.

Runtime On Demand Verbatim Corpus Observed

Purpose: Compare proposed tabular transformations against curated corpus-observed pattern guidance.
Trigger: When the data-flow brief proposes tabular filtering, projection, join, aggregation, SQL, or free-form text-processing sections.

Researchiwc-test-data-conventions

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Compare proposed test-data placement and fixture shapes against IWC conventions.
Trigger: When the design briefs hint at workflow tests or input fixture organization.

Researchiwc-shortcuts-anti-patterns

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Flag proposed shortcuts that are accepted in IWC versus shortcuts that should be treated as smells.
Trigger: When the design briefs propose tests, assertions, labels, or expected-output comparisons.

Cast artifacts

Claude skillcompare-against-iwc-exemplar— Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.

How to install →

Artifact handoffs

/ pipeline contract

Produces

iwc-comparison-notes markdown iwc-comparison-notes.md

Structural diff against the nearest IWC exemplar(s); guidance for the downstream *-summary-to-galaxy-template Mold before per-step authoring.
consumed by

Consumes

nextflow-galaxy-interface

Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] when running the NEXTFLOW → GALAXY pipeline.
produced by
- nextflow-summary-to-galaxy-interface
nextflow-galaxy-data-flow

Galaxy data-flow brief from [[nextflow-summary-to-galaxy-data-flow]] when running the NEXTFLOW → GALAXY pipeline.
produced by
- nextflow-summary-to-galaxy-data-flow
cwl-galaxy-interface

Galaxy interface brief from [[cwl-summary-to-galaxy-interface]] when running the CWL → GALAXY pipeline.
produced by
- cwl-summary-to-galaxy-interface
cwl-galaxy-data-flow

Galaxy data-flow brief from [[cwl-summary-to-galaxy-data-flow]] when running the CWL → GALAXY pipeline.
produced by
- cwl-summary-to-galaxy-data-flow
paper-galaxy-design

Combined Galaxy interface + data-flow design brief from [[paper-summary-to-galaxy-design]] when running the PAPER → GALAXY pipeline.
produced by
- paper-summary-to-galaxy-design

compare-against-iwc-exemplar

Find the nearest IWC exemplar workflow(s) for the upstream Galaxy design briefs and emit a structural diff that guides the downstream *-summary-to-galaxy-template Mold before per-step authoring effort is spent.

This Mold is the corpus-first check in Galaxy-targeting pipelines. It runs after the source-specific interface and data-flow briefs (or the combined paper design brief) and before the gxformat2 template Mold. Discovery, ranking, and comparison are one action — there is no separate retrieval Mold.

Procedure

Clone or pull and merge the IWC <url> to ~/.foundry/iwc.
Normalize candidate workflows with convert as needed for structural comparison.
Find the closest workflow and rank it.

Feature Hierarchy

Domain or analysis intent.
Input collection topology.
Primary tool families.
DAG motifs and structural recipes.
Output types and report shape.
Test style and fixture topology.

Domain comes first so a structurally similar workflow in the wrong science area does not become a misleading exemplar. Topology comes second because collection shape is one of the most important Galaxy-specific design decisions. Test style is useful after a workflow match, but should not drive initial retrieval. Briefs with no domain signal should not produce a high-confidence exemplar even if they share generic tools.

Confidence Levels

Level	Meaning
High	Same domain/subdomain, same input topology, same primary tool families, same major DAG motifs, and matching test fixture shape.
Medium	Same domain and topology, but partial tool-family or output match. Useful exemplar, not canonical.
Low	Cross-domain structural match only. Useful for a pattern comparison, not a nearest domain exemplar.
No nearest exemplar	Candidate lacks domain or topology alignment, or only shares generic tools such as MultiQC.

Routing findings forward

Each finding should name the authoring surface most likely to own the fix:

Template/data-flow issue: missing node, wrong collection shape, wrong branch, placeholder too vague — surfaced for the downstream *-summary-to-galaxy-template Mold to apply.
Pattern issue: recurring Galaxy idiom should become or update a pattern page.
Tool-step issue: exact wrapper or parameterization will be handled later in the per-step loop.
Test issue: defer to *-test-to-galaxy-test-plan or implement-galaxy-workflow-test.

Do not block downstream authoring on low-confidence exemplar mismatches. Report them as review guidance for the template Mold and the user.

Non-goals

No tool discovery. Do not replace discover-shed-tool.
No automatic rewrite. This Mold emits structural diff guidance; the harness or user decides which changes to apply.
No forced nearest. A no-match result is valid when IWC lacks a close exemplar.

Incoming References (9)

Galaxy: collection patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy collection transformation patterns.
Galaxy: conditionals patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns.
Galaxy: tabular patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
CWL → GALAXYphase of pipeline— Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
PAPER → GALAXYphase of pipeline— Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
CWL when:/pickValue → Galaxy branching translationrelated mold— CWL `when:`/`pickValue` → Galaxy. Three honest translations (paired_or_unpaired input, native pick_value step, sibling workflows) plus how to pick among them.
Galaxy data-flow draft contractrelated mold— Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
Galaxy workflow draft formatrelated mold— gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.