Map a Nextflow summary into a CWL Workflow interface design brief.
/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundryThen invoke as:
/foundry-skills:nextflow-summary-to-cwl-interfacecodex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundryThen select with /skills or invoke explicitly as:
$nextflow-summary-to-cwl-interfaceProduces: 1 artifact.
Consumes: 1 artifact.
Reviewable Markdown brief: CWL Workflow inputs, outputs, labels, array/record/File shapes, checkpoint outputs, source provenance.
{
"id": "nextflow-cwl-interface",
"kind": "markdown",
"default_filename": "nextflow-cwl-interface.md",
"description": "Reviewable Markdown brief: CWL Workflow inputs, outputs, labels, array/record/File shapes, checkpoint outputs, source provenance."
}Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for CWL interface choices.
{
"id": "summary-nextflow",
"description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for CWL interface choices.",
"inherited_schema": "[[summary-nextflow]]",
"producers": [
"summarize-nextflow"
]
}Read source-level channel, parameter, process, and test-fixture evidence before choosing CWL Workflow inputs and outputs.
references/schemas/summary-nextflow.schema.jsonpackage://@galaxy-foundry/summarize-nextflow#summaryNextflowSchema{
"$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-interface
Follow the procedure below and use the artifact/reference sections as the runtime contract.
## When To Use
- Map a Nextflow summary into a CWL Workflow interface design brief.
## Inputs
- Read artifact `summary-nextflow`. Schema: summary-nextflow. Produced by `summarize-nextflow`. Structured Nextflow pipeline summary emitted by summarize-nextflow; the source-of-truth JSON for CWL interface choices.
## Outputs
- Write artifact `nextflow-cwl-interface` as `nextflow-cwl-interface.md`. Format: `markdown`. Reviewable Markdown brief: CWL Workflow inputs, outputs, labels, array/record/File shapes, checkpoint outputs, source 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 source-level channel, parameter, process, and test-fixture evidence before choosing CWL Workflow inputs and outputs.
## Load On Demand
- None declared.
## Validation
- None declared.
## Procedure
Read a Nextflow summary and emit a reviewable Markdown interface brief for a CWL Workflow. Capture workflow inputs, workflow outputs, labels, array/record/File shapes, checkpoint outputs worth exposing for tests, source-summary provenance, confidence, and open questions.
The output is a design handoff consumed by nextflow-summary-to-cwl-data-flow, summary-to-cwl-template, and later test-plan work.
## Feedback Mode
- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.
## 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.