Home Mold

implement-galaxy-workflow-test

Assemble Galaxy workflow test fixtures and assertions.

draft mold target/galaxy

Related: galaxy-workflow-testability-design
iwc-test-data-conventions
iwc-shortcuts-anti-patterns
planemo-asserts-idioms
tests-format

Mold health

ok

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
8 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: implement-galaxy-workflow-test

contract

Reference Loading

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

CLI Commandvalidate-tests

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

Runtime On Demand Sidecar Corpus Observed

Purpose: Run the cheap static workflow-test validation and workflow-label cross-check before Planemo execution.
Trigger: After authoring or editing a Galaxy workflow test file and before Planemo invocation.

CLI Toolplanemo

Tool-level install metadata. Aggregated into the cast bundle's Required Tools section.

Runtime Upfront Verbatim Corpus Observed

Purpose: Runtime for workflow_test_init / workflow_test_on_invocation; install before authoring tests against a live invocation.

Schematests-format

Structured contract copied for validation or lookup.

Runtime Upfront Verbatim Corpus Observed

Purpose: JSON Schema contract for the Galaxy workflow test format. Output of this Mold must validate against it.

Researchgalaxy-workflow-testability-design

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Revise workflow inputs, outputs, labels, checkpoints, and collection identifiers so meaningful tests can be authored.
Trigger: When test authoring reveals missing labels, omitted workflow-level outputs, unstable collection identifiers, weakly assertable final outputs, or fixture-shape pressure on workflow inputs.

Researchiwc-test-data-conventions

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Assemble job input fixtures, remote URLs, hashes, collection shapes, and test-data layout in IWC style.
Trigger: When writing or revising the job/input side of a Galaxy workflow test file.

Researchplanemo-asserts-idioms

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Choose assertion families, tolerance magnitudes, and the static/Planemo validation loop.
Trigger: When writing or revising output assertions for a Galaxy workflow test file.

Researchiwc-shortcuts-anti-patterns

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Flag assertion shortcuts that are acceptable in IWC versus shortcuts that should be avoided.
Trigger: When considering existence-only, size-only, image-only, checksum, output-label, or negative-test patterns.

Researchplanemo-workflow-test-architecture

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: Write tests with stable labels and artifacts that Planemo can connect back to Galaxy invocations, jobs, and outputs.
Trigger: When adding or revising workflow tests that will be iterated with Planemo or generated from existing invocations.

Cast artifacts

Claude skillimplement-galaxy-workflow-test— Assemble Galaxy workflow test fixtures and assertions.

How to install →

Artifact handoffs

/ pipeline contract

Produces

galaxy-workflow-test yaml galaxy-workflow-tests.yml

Galaxy workflow test file (tests-format) with job inputs, expected outputs, assertions; passes static schema + label cross-check.

Consumes

galaxy-test-plan

Reviewable Galaxy test plan from a *-test-to-galaxy-test-plan Mold; profile, fixtures, snapshot/assertion provenance.
produced by
- cwl-test-to-galaxy-test-plan
- nextflow-test-to-galaxy-test-plan
galaxy-workflow-draft

gxformat2 workflow being tested; provides labels, outputs, and shapes the test must assert against.
produced by
test-data-refs

Resolved test data references (URLs, paths, expected shapes) from paper-to-test-data or find-test-data.
produced by
- find-test-data
- paper-to-test-data

implement-galaxy-workflow-test

Assemble a Galaxy workflow test file (tests-format) from the test plan, the gxformat2 draft, and the resolved test-data refs. One invocation produces a *-tests.yml whose job inputs come from the draft’s workflow inputs and whose assertions come from the test plan’s snapshots. The output must validate against tests-format and pass the workflow-label cross-check before any Planemo run.

The draft is the contract: input and output labels in the test file must address real workflow input/output labels. When authoring reveals a missing label, an omitted workflow output, or an unstable collection identifier, treat it as testability pressure on the workflow itself — surface it per galaxy-workflow-testability-design rather than asserting around it.

Sequence

Bootstrap. Prefer generating the test skeleton from a real invocation, not from scratch:
- planemo workflow_test_init --from_invocation <id> (planemo-workflow_test_init) — preferred bootstrap for new test files; reviewer convention. See planemo-asserts-idioms §7.
- planemo workflow_test_on_invocation <tests.yml> <id> (planemo-workflow_test_on_invocation) — fast assertion-iteration loop without re-running the workflow.
Author job inputs. Wire each workflow input to a test-data-refs entry. Follow iwc-test-data-conventions for remote-URL-first fixtures, recorded hashes, and per-input collection layout. Inputs must match the draft’s collection shapes and datatypes.
Author assertions. Translate the test plan’s snapshots into output assertions. Choose assertion families and tolerances per planemo-asserts-idioms; check each shortcut against iwc-shortcuts-anti-patterns so an existence-only or size-only assertion is a deliberate choice, not an evasion.
Validate static. Run validate-tests for the schema gate, then the workflow-label cross-check (checkTestsAgainstWorkflow): zero missing input labels, zero missing output labels, no collection/datatype mismatches. Fix before spending a Planemo run.
Run green. Drive planemo test on a managed Galaxy with the staged data and tools. On green, hand off the test file plus enough invocation/job/assertion context for run-workflow-test and debug-galaxy-workflow-output to use if a later run fails.

Author tests with stable labels and artifacts that Planemo can connect back to Galaxy invocations, jobs, and outputs (planemo-workflow-test-architecture) — that traceability is what makes the downstream debug Mold able to locate failure evidence.

Incoming References (12)

CWL → GALAXYphase of pipeline— Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
INTERVIEW → GALAXYphase of pipeline— Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
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.
Component Nextflow Testingrelated mold— nf-test patterns mapped to Galaxy planemo asserts and CWL test equivalents — backs nextflow-test-to-target-tests Mold and summarize-nextflow §7.
Galaxy Workflow Testability Designrelated note— Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible.
Iwc Shortcuts Anti Patternsrelated note— What IWC test suites cut corners on (accepted) vs what's a code smell — existence-only probes, sim_size deltas, image dim checks, label coupling.
Iwc Test Data Conventionsrelated note— How IWC workflows organize and reference test data — Zenodo-first, SHA-1 integrity, collection shapes, CVMFS gotchas.
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.
Planemo Asserts Idiomsrelated note— Decision and idiom guide for picking planemo workflow-test assertions: which family per output type, how to size tolerances, when to validate.
Planemo workflow-test architecturerelated mold— Reference for Planemo workflow test/run architecture, Galaxy modes, API polling, and noisy failure boundaries.
Galaxy workflow test formatrelated note— JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.