Translate a Nextflow summary into a CWL data-flow design brief.
/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundryThen invoke as:
/foundry-skills:nextflow-summary-to-cwl-data-flowcodex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundryThen select with /skills or invoke explicitly as:
$nextflow-summary-to-cwl-data-flowProduces: 1 artifact.
Consumes: 2 artifacts.
Reviewable Markdown brief: abstract topology, scatter/gather choices, value transformations, unresolved CommandLineTool needs, confidence.
{
"id": "nextflow-cwl-data-flow",
"kind": "markdown",
"default_filename": "nextflow-cwl-data-flow.md",
"description": "Reviewable Markdown brief: abstract topology, scatter/gather choices, value transformations, unresolved CommandLineTool needs, confidence."
}Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; consumed alongside the CWL interface brief.
{
"id": "summary-nextflow",
"description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; consumed alongside the CWL interface brief.",
"inherited_schema": "[[summary-nextflow]]",
"producers": [
"summarize-nextflow"
]
}Preceding CWL interface brief from [[nextflow-summary-to-cwl-interface]] that pins inputs, outputs, and labels.
{
"id": "nextflow-cwl-interface",
"description": "Preceding CWL interface brief from [[nextflow-summary-to-cwl-interface]] that pins inputs, outputs, and labels.",
"producers": [
"nextflow-summary-to-cwl-interface"
]
}Read process, channel, operator, and fixture structure while drafting CWL-facing abstract data flow.
references/schemas/summary-nextflow.schema.jsonpackage://@galaxy-foundry/summarize-nextflow#summaryNextflowSchema{
"$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
...
# nextflow-summary-to-cwl-data-flow
Follow the procedure below and use the artifact/reference sections as the runtime contract.
## When To Use
- Translate a Nextflow summary into a CWL data-flow design brief.
## Inputs
- Read artifact `summary-nextflow`. Schema: summary-nextflow. Produced by `summarize-nextflow`. Structured Nextflow pipeline summary emitted by summarize-nextflow; consumed alongside the CWL interface brief.
- Read artifact `nextflow-cwl-interface`. Produced by `nextflow-summary-to-cwl-interface`. Preceding CWL interface brief from nextflow-summary-to-cwl-interface that pins inputs, outputs, and labels.
## Outputs
- Write artifact `nextflow-cwl-data-flow` as `nextflow-cwl-data-flow.md`. Format: `markdown`. Reviewable Markdown brief: abstract topology, scatter/gather choices, value transformations, unresolved CommandLineTool needs, confidence.
## 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 process, channel, operator, and fixture structure while drafting CWL-facing abstract data flow.
## Load On Demand
- None declared.
## Validation
- None declared.
## Procedure
Read a Nextflow summary plus the preceding CWL interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, CWL scatter/gather choices, value transformations, unresolved CommandLineTool needs, confidence, and open questions.
The output is not a concrete CWL Workflow. summary-to-cwl-template turns this handoff and the interface brief into a skeleton.
## 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.