nextflow-to-test-data

name	nextflow-to-test-data
description	Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.

nextflow-to-test-data

Follow the procedure below and use the artifact/reference sections as the runtime contract.

When To Use

• Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.

Inputs

• Read artifact summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Structured Nextflow summary from summarize-nextflow; carries the selected profile's test_fixtures and the full nf_tests[] enumeration — each declared input a role plus url/path, sha1, and filetype.
• Read artifact nextflow-galaxy-interface. Produced by nextflow-summary-to-galaxy-interface. Galaxy interface brief from nextflow-summary-to-galaxy-interface pinning the workflow input labels, collection shapes, and datatypes each resolved fixture must map onto.

Outputs

• Write artifact test-data-refs as test-data-refs.json. Format: json. Test data resolved from the pipeline's declared fixtures, expressed as URLs/paths plus expected shapes for downstream test authoring. Shared id with find-test-data — the branch's search fallback fills only the inputs this Mold leaves unresolved.

Required Tools

• None declared. Procedure should not assume external CLIs are present.

Load Upfront

• references/schemas/summary-nextflow.schema.json: Schema file copied verbatim into the bundle. Input contract: read the selected profile's test_fixtures.inputs[] and the nf_tests[] enumeration — role, url/path, sha1, filetype — as the declared source of test data.

Load On Demand

• references/notes/component-nextflow-testing.md: Research note copied verbatim into the bundle. Interpret nf-test profiles and fixture conventions before mapping declared fixtures onto Galaxy inputs. Use when: reading test_fixtures / nf_tests to decide which profile's fixtures best cover the workflow inputs.
• references/notes/component-nextflow-testing.yml: Companion file copied verbatim into the bundle. Sibling of references/notes/component-nextflow-testing.md; read it where that note directs.
• references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Map each declared fixture to an addressable Galaxy input label and the collection shape it must populate. Use when: mapping a declared fixture (often a samplesheet-driven input) onto a Galaxy input's collection shape.
• references/notes/iwc-test-data-conventions.md: Research note copied verbatim into the bundle. Express each ref remote-URL-first with SHA-1 integrity and per-input collection layout when recording resolved fixtures. Use when: writing each test-data-refs entry.

Validation

• None declared.

Procedure

Resolve the Nextflow pipeline's own declared test fixtures into Galaxy test-data-refs. The Nextflow summary already carries the test-profile fixtures (test_fixtures) and the full nf-test enumeration (nf_tests[]) — each declared input a role plus a url/path, sha1, and filetype. Map those onto the Galaxy workflow's inputs and emit one ref per input, ready for implement-galaxy-workflow-test to stage.

This skill is the source-specific first leg of the harness's test-data-resolution branch. It resolves what the pipeline itself declares; any input it cannot resolve from a declared fixture stays a reported gap and the harness falls through to find-test-data (search), then to user-supplied. Deciding to fall through is a harness concern, not this skill's — its job is an honest map of the pipeline's own fixtures.

Sequence

1. Enumerate Galaxy inputs and their required shape. From the interface brief, list each workflow input: label, Galaxy collection shape (File / list / paired / list:paired / record), and datatype. This is the target shape every ref must satisfy.
2. Read the declared fixtures. From the summary's test_fixtures.inputs[] (selected profile) and nf_tests[] (other profiles), collect each declared input: role, url/path, sha1, filetype, and description. Prefer the profile whose fixtures best cover the workflow's inputs.
3. Map each declared fixture onto a Galaxy input. Match by role and shape onto the interface's input labels. A samplesheet-driven Nextflow input often expands into a Galaxy collection — record the element identifiers and any split/concatenation prep needed to reach the Galaxy collection shape (galaxy-workflow-testability-design).
4. Emit refs. Write one test-data-refs.json entry per resolved input: prefer the declared remote url + sha1 (remote-URL-first, iwc-test-data-conventions); fall back to the in-tree path plus provenance only when no URL is published. Carry datatype, collection element identifiers, and any subset/split prep. Each entry maps to an addressable workflow input label.
5. Report genuine gaps. An input with no declared fixture of the right shape stays resolved: false with a reason — this is what the harness hands to find-test-data. Do not search public sources here; searching is find-test-data's job, not this skill's.

No fabrication

Never invent a URL, accession, or path, and never emit a placeholder for an input you could not resolve from a declared fixture. A declared fixture with no published URL is recorded by its in-tree path plus provenance, not papered over with a guessed URL. Every emitted ref points at data the pipeline actually declares; everything else is an honest gap for the next leg of the branch.

Runtime Notes

• Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
• Preserve declared artifact filenames unless the user or harness supplies explicit paths.
• Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.