Foundry
Agent Skill · cast

nextflow-test-to-cwl-test-plan

Translate Nextflow test evidence into a CWL workflow test plan.

← All cast skills · Source mold →

Install with Claude Code

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Then invoke as:

/foundry-skills:nextflow-test-to-cwl-test-plan

Install with Codex

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

Then select with /skills or invoke explicitly as:

$nextflow-test-to-cwl-test-plan

Skill Bundle

/ packaged cast
attached files
1
upfront
1
on demand
0
cast rev
n/a
validated
0

Produces: 1 artifact.

Consumes: 1 artifact.

Artifact Contract

/ skill handoff

Produces

cwl-test-plan

Reviewable CWL workflow test plan: job inputs, expected outputs, assertions, fixtures, rationale provenance.

markdowncwl-test-plan.md
Raw artifact contract 
{
  "id": "cwl-test-plan",
  "kind": "markdown",
  "default_filename": "cwl-test-plan.md",
  "description": "Reviewable CWL workflow test plan: job inputs, expected outputs, assertions, fixtures, rationale provenance."
}

Consumes

summary-nextflow

Structured Nextflow summary from [[summarize-nextflow]]; carries test_fixtures, nf_tests, snapshot evidence.

Raw artifact contract 
{
  "id": "summary-nextflow",
  "description": "Structured Nextflow summary from [[summarize-nextflow]]; carries test_fixtures, nf_tests, snapshot evidence.",
  "inherited_schema": "[[summary-nextflow]]",
  "producers": [
    "summarize-nextflow"
  ]
}

Attached Files

/ runtime references

Load upfront

schema

summary-nextflow

packaged

Read summarized nf-test profiles, snapshot fixtures, selected test data, params, and expected outputs.

upfront runtime verbatim corpus-observed deterministic 58.7 KB
bundle
references/schemas/summary-nextflow.schema.json
source
package://@galaxy-foundry/summarize-nextflow#summaryNextflowSchema
Preview json 
{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/summary-nextflow.schema.json",
  "$comment": "Canonical source: packages/summarize-nextflow/src/schema/summary-nextflow.schema.json in galaxyproject/foundry. Mold frontmatter cites this schema via [[summary-nextflow]] wiki-links; the cast pipeline imports the `summaryNextflowSchema` runtime export and serializes it into cast bundles.",
  "title": "Nextflow Pipeline Summary",
  "description": "Structured per-source summary emitted by the summarize-nextflow Mold.\n\nPer-source schema by design — paper, Nextflow, and CWL each have their own summary shape; downstream Molds (data flow, templates, tool wrappers) consume any source's summary and handle the polymorphism.\n\nField names mirror gxy-sketches' SketchSource / ToolSpec / TestDataRef / ExpectedOutputRef where parity exists; see content/research/gxy-sketches-alignment/index.md.",
  "$ref": "#/$defs/Summary",
  "$defs": {
    "Summary": {
      "title": "Summary",
      "description": "Top-level shape. Every Nextflow summary is exactly this object.",
      "type": "object",
      "additionalProperties": false,
      "required": [
        "source",
        "params",
        "sample_sheets",
        "profiles",
        "tools",
        "processes",
        "subworkflows",
        "workflow",
        "reference_assets",
        "reference_rebuilds",
        "test_fixtures",
        "nf_tests"
      ],
      "properties": {
        "source": {
          "$ref": "#/$defs/SourceRecord"
        },
        "params": {
          "type": "array",
          "items": {
            "$ref": "#/$defs/Param"
          }
        },
        "sample_sheets": {
          "type": "array",
          "items": {
            "$ref": "#/$defs/SampleSheet"
          },
          "description": "Structured sample-sheet inputs. Each entry binds one `params[]` parameter to a row schema (column names, types, path-vs-meta classification, required flags, enums, patterns). Promoted from prose inside `params[].description` so downstream target translations (Galaxy `sample_sheet*` collections, CWL records-of-arrays) can choose collection variants without re-parsing the source pipeline. Empty array when no sample-sheet idiom is detected. Discovery sources: nf-schema `schema:` references, `samplesheetToList()` calls, and `splitCsv(header
...

SKILL.md


# nextflow-test-to-cwl-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 CWL 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 `cwl-test-plan` as `cwl-test-plan.md`. Format: `markdown`. Reviewable CWL workflow test plan: job inputs, expected outputs, assertions, fixtures, rationale provenance.

## Required Tools

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

## Load Upfront

- `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

- None declared.

## Validation

- None declared.

## Procedure

Translate Nextflow test evidence into a CWL workflow test plan. This preserves the `NEXTFLOW → CWL` pipeline after the Galaxy-specific test-plan split; concrete CWL test artifact assembly remains owned by implement-cwl-workflow-test.

## 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.