Home Mold

nextflow-test-to-galaxy-test-plan

Translate Nextflow test evidence into a Galaxy workflow test plan.

draft mold source/nextflow

Related: galaxy-workflow-test-plan
summary-nextflow
tests-format

Mold health

ok

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 declares properties and check type.
eval.md ↗
Scenarios
Concrete cases: fixtures bound to expected values, run against the eval properties.

scenarios.md declares cases bound to fixtures.
scenarios.md ↗
Typed refs
8 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-test-to-galaxy-test-plan

contract

Reference Loading

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

Schemagalaxy-workflow-test-plan

Structured contract copied for validation or lookup.

Runtime Upfront Verbatim Hypothesis

Purpose: Output contract: the emitted plan conforms to [[galaxy-workflow-test-plan]]. Cast bundles the JSON Schema; validate with `foundry validate-galaxy-workflow-test-plan`.
Verify: Cast the skill on an nf-core/bacass summary and confirm the emitted YAML validates and downstream [[implement-galaxy-workflow-test]] consumes it.

Schemasummary-nextflow

Structured contract copied for validation or lookup.

Runtime Upfront Verbatim Corpus Observed

Purpose: Read summarized nf-test profiles, snapshot fixtures, selected test data, params, and expected outputs.

Schematests-format

Structured contract copied for validation or lookup.

Runtime On Demand Verbatim Corpus Observed

Purpose: Use the Galaxy workflow tests schema as the assertion vocabulary when translating Nextflow test evidence into a Galaxy test plan.
Trigger: When mapping expected outputs, tolerances, snapshots, or fixture assertions into Galaxy workflow-test assertion intent.

Researchcomponent-nextflow-testing

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Hypothesis

Purpose: Interpret nf-test profiles, snapshot assertions, and Nextflow fixture conventions before translating them.
Trigger: When converting nf_tests, snapshot fixtures, test profiles, or source test-data references into a Galaxy workflow test plan.
Verify: Translate nf-core/bacass nf-test snapshots into a Galaxy test plan and confirm this note improves profile/snapshot extraction.

Researchiwc-test-data-conventions

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Emit Galaxy/IWC-style job input fixtures, remote locations, hashes, and collection input shapes.
Trigger: When writing job inputs or deciding whether fixtures belong in test-data, Zenodo, ENA/SRA, or CVMFS.

Researchplanemo-asserts-idioms

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Describe Galaxy workflow-test assertion intent and tolerances for translated expected outputs.
Trigger: When turning Nextflow expected outputs or snapshots into Galaxy test-plan assertions.

Researchnextflow-snapshot-to-galaxy-assertions

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Translate nf-test snapshot captures, helper-pruned file lists, and snapshot checksums into Galaxy workflow-test assertion intent.
Trigger: When converting nf-test snapshot fixtures, .snap sidecars, ignore files, ignore globs, or pipeline-level stable path/name captures.

Researchiwc-shortcuts-anti-patterns

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Distinguish accepted IWC-style test shortcuts from assertion smells while translating tests.
Trigger: When deciding whether to use existence-only, size-only, image-dimension, or tolerant output checks.

Artifact handoffs

/ pipeline contract

Produces

galaxy-test-plan yaml galaxy-test-plan.yml

Reviewable Galaxy workflow test plan (see [[galaxy-workflow-test-plan]]): profile, fixture, snapshot, ignored-file, expected-output, rationale provenance translated from nf-test evidence.
schema

galaxy-workflow-test-plan

consumed by
- implement-galaxy-workflow-test

Consumes

summary-nextflow

Structured Nextflow summary from [[summarize-nextflow]]; carries test_fixtures, nf_tests, snapshot evidence.
produced by
- summarize-nextflow

nextflow-test-to-galaxy-test-plan

Translate Nextflow test evidence into a Galaxy workflow test plan. The output is a reviewable YAML handoff conforming to galaxy-workflow-test-plan, not a concrete tests-format file: preserve profile, fixture, snapshot, ignored-file, expected-output, and rationale provenance so implement-galaxy-workflow-test can author the final Galaxy test artifact with the right labels and assertions. Because this plan is translated from real nf-test evidence, set source.derived_from: test-evidence and prefer evidence: test-evidence on the assertions it carries.

Incoming References (6)

changeset-to-galaxy-test-planrelated mold— Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
Nextflow nf-test snapshots to Galaxy/Planemo assertionsrelated mold— Translates nf-test snapshot assertions into Galaxy workflow test-format assertions, broken out by module-level vs pipeline-level test shape.
Galaxy workflow test planrelated note— JSON Schema for the intermediate Galaxy workflow test-plan handoff produced by the test-plan Molds and consumed by implement-galaxy-workflow-test.
Nextflow pipeline summaryrelated note— JSON Schema for the structured summary emitted by the summarize-nextflow Mold.
Galaxy workflow test formatrelated note— JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.