Foundry
Home Mold

nextflow-test-to-galaxy-test-plan

Translate Nextflow test evidence into a Galaxy workflow test plan.

reviewed source/nextflow
Related

Mold health

ok
  • Source layout

    Every file beside index.md is one the mold kind declares.

  • Axis fields

    source-specific fields are coherent.

  • Eval plan

    Abstract oracle: the properties any cast of this Mold must satisfy.

    eval.md declares properties and check type.

    eval.md ↗
  • Scenarios

    Concrete cases bound to fixtures, run against the eval properties.

    scenarios.md declares cases bound to fixtures.

    scenarios.md ↗
  • Typed refs

    9 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 references describe what casting consumes, and when the generated skill should load each artifact.

Schema galaxy-workflow-test-plan

Structured contract copied for validation or lookup.

RuntimeUpfrontVerbatimHypothesis
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.
Schema tests-format

Structured contract copied for validation or lookup.

RuntimeOn DemandVerbatimCorpus 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.
Research component-nextflow-testing

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimHypothesis
Purpose
Interpret nf-test profiles, snapshot assertions, and Nextflow fixture conventions before translating them.
Trigger
When converting test_candidates, 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.
Research nextflow-test-case-selection

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Preserve the upstream candidate-selection rationale and distinguish primary coverage from bootstrap-only or reference-scale cases.
Trigger
When the selected case is minimal, tiny, full-scale, stub-only, or accompanied by deferred whole-pipeline candidates.
Research iwc-test-data-conventions

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus 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.
Research nextflow-snapshot-to-galaxy-assertions

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus 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.

Cast artifacts

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

  • summary-nextflow

    Structured Nextflow summary from [[summarize-nextflow]]; carries test_candidates, test_selection, and snapshot evidence.

    produced by

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.

Consume the candidate selected by summarize-nextflow; do not re-rank profiles here. Use nextflow-test-case-selection to preserve whether that case is primary coverage, a topology bootstrap, or reference-scale evidence, and to keep deferred science branches visible rather than presenting one translated test as exhaustive.

Incoming References (8)

  • changeset-to-galaxy-test-plan related 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 → GALAXY phase of pipeline — Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
  • Component Nextflow Testing related mold — nf-test patterns mapped to Galaxy planemo asserts and CWL test equivalents — backs the nextflow test-plan Molds and summarize-nextflow §7.
  • Nextflow nf-test snapshots to Galaxy/Planemo assertions related mold — Translates nf-test snapshot assertions into Galaxy workflow test-format assertions, broken out by module-level vs pipeline-level test shape.
  • Selecting the first Nextflow test case related mold — A deterministic policy for choosing the first whole-pipeline Nextflow test case without mistaking profile names for coverage.
  • Galaxy workflow test plan related 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 summary related note — JSON Schema for the structured summary emitted by the summarize-nextflow Mold.
  • Galaxy workflow test format related note — JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.