nextflow-to-test-data

---
type: research
subtype: component
tags:
  - research/component
  - source/nextflow
component: "Nextflow Testing and Test Fixtures"
status: draft
created: 2026-05-01
revised: 2026-05-05
revision: 2
ai_generated: true
summary: "nf-test patterns mapped to Galaxy planemo asserts and CWL test equivalents — backs nextflow-test-to-target-tests Mold and summarize-nextflow §7."
companions:
  - "component-nextflow-testing.yml"
sources:
  - "https://www.nf-test.com/"
  - "https://www.nf-test.com/docs/assertions/"
  - "https://www.nf-test.com/docs/assertions/snapshots/"
  - "https://www.nf-test.com/docs/configuration/"
  - "https://nf-co.re/docs/contributing/nf-test/assertions"
  - "https://nf-co.re/docs/developing/testing/overview"
  - "https://github.com/nf-core/test-datasets"
  - "https://www.nextflow.io/docs/latest/config.html#config-profiles"
  - "https://nf-co.re/docs/contributing/pipelines#test-data"
related_molds:
  - "[[summarize-nextflow]]"
  - "[[nextflow-test-to-target-tests]]"
  - "[[implement-galaxy-workflow-test]]"
related_notes:
  - "[[planemo-asserts-idioms]]"
  - "[[tests-format]]"
  - "[[iwc-test-data-conventions]]"
  - "[[component-nf-core-tools]]"
---

# Nextflow Testing and Test Fixtures

Operational grounding for two Molds:

- [[summarize-nextflow]] §7 — extract `nf_tests[]` and `test_fixtures` from a real nf-core or DSL2 pipeline.
- [[nextflow-test-to-target-tests]] — translate nf-test fixtures + assertions into Galaxy / CWL equivalents.

The summarize side is mostly *enumeration*: walk `tests/*.nf.test`, extract structured fields per the Mold §7 spec. The translation side is *mapping*: each nf-test assertion pattern has a (sometimes lossy) Galaxy or CWL equivalent.

Companion structured form: `component-nextflow-testing.yml`. Per-pattern entries with `n
...

# nf-test patterns → Galaxy / CWL test equivalents.
# Companion to component-nextflow-testing.md.
#
# Rows ordered by frequency in real nf-core pipelines (snapshot block first).

mappings:

  # ---- Snapshot block (nf-core canonical idiom) ----

  - id: snapshot.match
    nf_test_pattern: "assert snapshot(...).match()"
    description: "Top-level snapshot assertion comparing serialized form of N captured values to a stored .nf.test.snap file."
    galaxy_equivalent: "Per-output assertion block in <workflow>-tests.yml; no single-line analog. Decompose into per-capture assertions (rows below)."
    cwl_equivalent: "cwltest expected_outputs entries per output; no single-line analog. Decompose."
    target_link: "[[tests-format]]"
    notes: "The whole-snapshot idiom is lossy on translation; explode into N per-capture assertions and accept the surface-area increase."

  - id: snapshot.succeeded_task_count
    nf_test_pattern: "workflow.trace.succeeded().size()"
    description: "Count of successfully completed tasks. nf-core canonical first capture; brittle across pipeline versions but stable per release."
    galaxy_equivalent: "Implicit in workflow execution success. Galaxy workflow tests pass iff the workflow completes; per-step success surfaces via has_text on log outputs."
    cwl_equivalent: "Implicit in cwltest's `should_succeed` / `should_fail` boolean. No per-task count."
    target_link: "[[planemo-asserts-idioms]] §1 (Plain text reports / logs)"
    notes: "Drop on translation; targets verify success implicitly."

  - id: snapshot.versions_yml
    nf_test_pattern: "ch_versions or path('versions.yml')"
    description: "The `versions` topic channel collected per process and dumped to versions.yml at workflow end. nf-core canonical second capture."
    galaxy_equiv
...

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-05-03
revised: 2026-05-06
revision: 2
ai_generated: true
related_notes:
  - "[[iwc-workflow-testability-survey]]"
  - "[[iwc-test-data-conventions]]"
  - "[[planemo-asserts-idioms]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[planemo-workflow-test-architecture]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[gxformat2-schema]]"
  - "[[gxformat2-workflow-inputs]]"
  - "[[galaxy-datatypes-conf]]"
summary: "Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible."
---

# Galaxy workflow testability design

Use this note when authoring or translating a Galaxy workflow **before** the `-tests.yml` file exists. It covers workflow structure choices that make later IWC-style tests meaningful: labels, promoted checkpoints, collection identifiers, and fixture-compatible inputs.

This is not a `content/patterns/` page. It is cross-cutting design guidance for Molds that need testable Galaxy workflows. Assertion syntax lives in [[planemo-asserts-idioms]]. Test YAML fixture shapes live in [[iwc-test-data-conventions]]. Accepted shortcut vs smell calls live in [[iwc-shortcuts-anti-patterns]]. Corpus evidence trail lives in [[iwc-workflow-testability-survey]].

## 1. Treat labels as API

Workflow input and output labels are not cosmetic. Planemo and IWC tests address workflow inputs and outputs by label, and the survey found exact label matches for every asserted output across 114 matched workflow/test pairs. A generated workflow should therefore pick stable, descriptive labels before test authoring starts.

Rules:

- Label every output that may need a test assertion.
- Treat input/output renames as breaking changes
...

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-03
revision: 3
ai_generated: true
related_notes:
  - "[[galaxy-workflow-testability-design]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[planemo-asserts-idioms]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[tests-format]]"
  - "[[iwc-tabular-operations-survey]]"
summary: "How IWC workflows organize and reference test data — Zenodo-first, SHA-1 integrity, collection shapes, CVMFS gotchas."
---

# IWC test data conventions

Reference for an agent implementing or editing a `<workflow>-tests.yml` in IWC style. All evidence cited from `/Users/jxc755/projects/repositories/workflow-fixtures/iwc-src/workflows/` (raw IWC clone) and `workflows/README.md`. Authoritative spec: [planemo.readthedocs.io/en/latest/test_format.html](https://planemo.readthedocs.io/en/latest/test_format.html). The companion analysis at `/Users/jxc755/projects/repositories/galaxy-brain/vault/projects/workflow_state/skills/COMPONENT_GALAXY_WORKFLOW_TESTING.md` is the synthesized source for several normative claims here.

This note owns **test YAML fixture shapes**. For workflow-structure choices that make those fixtures possible before the test file exists, use [[galaxy-workflow-testability-design]].

## 1. Where does test data live? Remote vs in-repo

Two storage patterns. They mix freely inside one job.

**Remote `location:` (default for any non-trivial input).** Strongly preferred for anything bigger than a toy fixture. Order of preference, observed in the corpus:

- **Zenodo** — overwhelming default, persistent DOI-backed URL.
  - `read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml:13,17` — `https://zenodo.org/records/11484
...