Structured contract copied for validation or lookup.
- Purpose
- Read summarized nf-test profiles, snapshot fixtures, selected test data, params, and expected outputs.
nextflow-test-to-galaxy-test-plan
Translate Nextflow test evidence into a Galaxy workflow test plan.
Mold health
ok- Source layout
Directory Mold with only index.md frontmatter.
- Axis fields
source-specific fields are coherent.
- Eval plan
eval.md declares cases and check type.
- Typed refs
7 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.
Structured contract copied for validation or lookup.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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 contractProduces
-
Reviewable Galaxy workflow test plan: profile, fixture, snapshot, ignored-file, expected-output, rationale provenance.
Consumes
-
Structured Nextflow summary from [[summarize-nextflow]]; carries test_fixtures, nf_tests, snapshot evidence.
nextflow-test-to-galaxy-test-plan
Translate Nextflow test evidence into a Galaxy workflow test plan. The output is a reviewable handoff, 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.
Incoming References (4)
- 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.
- 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`.