nextflow-test-to-galaxy-test-plan

name	nextflow-test-to-galaxy-test-plan
description	Translate Nextflow test evidence into a Galaxy workflow test plan.

nextflow-test-to-galaxy-test-plan

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

When To Use

• Translate Nextflow test evidence into a Galaxy workflow test plan.

Inputs

• Read artifact summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Structured Nextflow summary from summarize-nextflow; carries test_fixtures, nf_tests, snapshot evidence.

Outputs

• Write artifact galaxy-test-plan as galaxy-test-plan.yml. Format: yaml. Schema: galaxy-workflow-test-plan. Reviewable Galaxy workflow test plan (see galaxy-workflow-test-plan): profile, fixture, snapshot, ignored-file, expected-output, rationale provenance translated from nf-test evidence.

Required Tools

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

Load Upfront

• references/schemas/galaxy-workflow-test-plan.schema.json: Schema file copied verbatim into the bundle. Output contract: the emitted plan conforms to galaxy-workflow-test-plan. Cast bundles the JSON Schema; validate with foundry validate-galaxy-workflow-test-plan.
• references/schemas/summary-nextflow.schema.json: Schema file copied verbatim into the bundle. Read summarized nf-test profiles, snapshot fixtures, selected test data, params, and expected outputs.

Load On Demand

• references/notes/component-nextflow-testing.md: Research note copied verbatim into the bundle. Interpret nf-test profiles, snapshot assertions, and Nextflow fixture conventions before translating them. Use when: converting nf_tests, snapshot fixtures, test profiles, or source test-data references into a Galaxy workflow test plan.
• 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/iwc-shortcuts-anti-patterns.md: Research note copied verbatim into the bundle. Distinguish accepted IWC-style test shortcuts from assertion smells while translating tests. Use when: deciding whether to use existence-only, size-only, image-dimension, or tolerant output checks.
• references/notes/iwc-test-data-conventions.md: Research note copied verbatim into the bundle. Emit Galaxy/IWC-style job input fixtures, remote locations, hashes, and collection input shapes. Use when: writing job inputs or deciding whether fixtures belong in test-data, Zenodo, ENA/SRA, or CVMFS.
• references/notes/nextflow-snapshot-to-galaxy-assertions.md: Research note copied verbatim into the bundle. Translate nf-test snapshot captures, helper-pruned file lists, and snapshot checksums into Galaxy workflow-test assertion intent. Use when: converting nf-test snapshot fixtures, .snap sidecars, ignore files, ignore globs, or pipeline-level stable path/name captures.
• references/notes/planemo-asserts-idioms.md: Research note copied verbatim into the bundle. Describe Galaxy workflow-test assertion intent and tolerances for translated expected outputs. Use when: turning Nextflow expected outputs or snapshots into Galaxy test-plan assertions.
• references/schemas/tests-format.schema.json: Schema file copied verbatim into the bundle. Use the Galaxy workflow tests schema as the assertion vocabulary when translating Nextflow test evidence into a Galaxy test plan. Use when: mapping expected outputs, tolerances, snapshots, or fixture assertions into Galaxy workflow-test assertion intent.

Validation

• Validate galaxy-test-plan.yml before returning it: run foundry validate-galaxy-workflow-test-plan galaxy-test-plan.yml from @galaxy-foundry/foundry. If the command is not on PATH, run npx --package @galaxy-foundry/foundry foundry validate-galaxy-workflow-test-plan galaxy-test-plan.yml. This checks artifact galaxy-test-plan against the galaxy-workflow-test-plan schema.

Procedure

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.

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.