Structured contract copied for validation or lookup.
- Purpose
- 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.
nextflow-to-test-data
Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.
Mold health
warn- Source layout
Directory Mold with only index.md frontmatter.
- Axis fields
source-specific fields are coherent.
- Eval plan
Abstract oracle: fixture-independent property checks any run must satisfy.
eval.md not written yet.
- Scenarios
Concrete cases: fixtures bound to expected values, run against the eval properties.
scenarios.md not written yet.
- Typed refs
4 typed references; 0 resolver issues.
- On-demand triggers
All on-demand references describe triggers.
- Evidence checks
Hypothesis references include verification.
- axis
- source-specific
- source
- nextflow
- name
- nextflow-to-test-data
contract
Reference Loading
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Interpret nf-test profiles and fixture conventions before mapping declared fixtures onto Galaxy inputs.
- Trigger
- When reading `test_fixtures` / `nf_tests` to decide which profile's fixtures best cover the workflow inputs.
- Verify
- Map nf-core/bacass declared fixtures onto its Galaxy interface and confirm this note improves profile/fixture selection.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Map each declared fixture to an addressable Galaxy input label and the collection shape it must populate.
- Trigger
- When mapping a declared fixture (often a samplesheet-driven input) onto a Galaxy input's collection shape.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Express each ref remote-URL-first with SHA-1 integrity and per-input collection layout when recording resolved fixtures.
- Trigger
- When writing each `test-data-refs` entry.
Cast artifacts
- Claude skillnextflow-to-test-data— Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.
Artifact handoffs
/ pipeline contractProduces
-
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.
Consumes
-
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.
-
Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] pinning the workflow input labels, collection shapes, and datatypes each resolved fixture must map onto.
nextflow-to-test-data
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 Mold 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 Mold’s — its job is an honest map of the pipeline’s own fixtures.
Sequence
- 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.
- Read the declared fixtures. From the summary’s
test_fixtures.inputs[](selected profile) andnf_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. - 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).
- Emit refs. Write one
test-data-refs.jsonentry per resolved input: prefer the declared remoteurl+sha1(remote-URL-first, iwc-test-data-conventions); fall back to the in-treepathplus 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. - Report genuine gaps. An input with no declared fixture of the right shape stays
resolved: falsewith 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 Mold’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.
Incoming References (1)
- NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.