Map a Nextflow summary into a Galaxy workflow interface design brief.
/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundryThen invoke as:
/foundry-skills:nextflow-summary-to-galaxy-interfacecodex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundryThen select with /skills or invoke explicitly as:
$nextflow-summary-to-galaxy-interfaceProduces: 2 artifacts.
Consumes: 3 artifacts.
Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance.
{
"id": "nextflow-galaxy-interface",
"kind": "markdown",
"default_filename": "nextflow-galaxy-interface.md",
"description": "Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance."
}Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
{
"id": "open-requirements-ledger",
"kind": "yaml",
"default_filename": "open-requirements.ledger.yml",
"description": "Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact."
}Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for interface choices.
{
"id": "summary-nextflow",
"description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for interface choices.",
"inherited_schema": "[[summary-nextflow]]",
"producers": [
"summarize-nextflow"
]
}Reference-data shape brief from [[nextflow-summary-to-galaxy-reference-data]] that pins per-asset reference inputs and rebuild-on-absence behavior.
{
"id": "nextflow-galaxy-reference-data",
"description": "Reference-data shape brief from [[nextflow-summary-to-galaxy-reference-data]] that pins per-asset reference inputs and rebuild-on-absence behavior.",
"producers": [
"nextflow-summary-to-galaxy-reference-data"
]
}Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
{
"id": "open-requirements-ledger",
"description": "Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.",
"producers": [
"advance-galaxy-draft-step",
"apply-galaxy-workflow-changeset",
"compare-against-iwc-exemplar",
"cwl-summary-to-galaxy-data-flow",
"cwl-summary-to-galaxy-interface",
"cwl-summary-to-galaxy-template",
"freeform-summary-to-galaxy-data-flow",
"freeform-summary-to-galaxy-interface",
"freeform-summary-to-galaxy-template",
"implement-galaxy-tool-step",
"interview-to-galaxy-workflow-changeset",
"nextflow-summary-to-galaxy-data-flow",
"nextflow-summary-to-galaxy-interface",
"nextflow-summary-to-galaxy-reference-data",
"nextflow-summary-to-galaxy-template",
"repair-galaxy-draft-topology"
]
}Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.
references/notes/nextflow-params-to-galaxy-inputs.mdcontent/research/nextflow-params-to-galaxy-inputs/index.md---
type: research
title: "Nextflow params to Galaxy workflow inputs"
tags:
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-08
revision: 4
related_notes:
- "[[nextflow-workflow-io-semantics]]"
- "[[gxformat2-workflow-inputs]]"
- "[[galaxy-sample-sheet-collections]]"
- "[[nextflow-path-glob-to-galaxy-datatype]]"
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[galaxy-workflow-testability-design]]"
- "[[galaxy-collection-semantics]]"
- "[[summary-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
related_molds:
- "[[summarize-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
- "https://www.nextflow.io/docs/latest/cli.html#pipeline-parameters"
- "https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/"
- "https://nextflow-io.github.io/nf-schema/latest/samplesheets/samplesheetToList/"
- "https://github.com/galaxyproject/gxformat2/blob/main/schema/v19_09/workflow.yml"
- "https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/workflow/modules.py"
summary: "Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs."
---
# Nextflow params to Galaxy workflow inputs
Use this note when [[nextflow-summary-to-galaxy-interface]] turns a [[summary-nextflow]] artifact into Galaxy workflow inputs. [[nextflow-workflow-io-semantics]] defines what counts as a Nextflow interface surface; this note narrows that into gxformat2 input decisions.
Evidence quality:
- **Corpus-observed** claims cite pinned fixtures under `$NEXTFLOW_FIXTURES`, the shared clone at `/Users/jxc755/projects/repositories/workflow-fixtures
...Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.
references/notes/nextflow-path-glob-to-galaxy-datatype.mdcontent/research/nextflow-path-glob-to-galaxy-datatype/index.md---
type: research
title: "Nextflow path/glob to Galaxy datatype mapping"
tags:
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-06
revision: 1
related_notes:
- "[[nextflow-workflow-io-semantics]]"
- "[[gxformat2-workflow-inputs]]"
- "[[galaxy-datatypes-conf]]"
- "[[galaxy-sample-sheet-collections]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[summary-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
related_molds:
- "[[summarize-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
- "content/research/galaxy-datatypes-conf/datatypes_conf.xml.sample"
- "https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/config/datatypes_conf.xml.sample"
- "https://www.nextflow.io/docs/latest/process.html"
- "https://www.nextflow.io/docs/latest/reference/channel.html"
- "https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/"
summary: "Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions."
---
# Nextflow path/glob to Galaxy datatype mapping
Use this note when a Nextflow-to-Galaxy Mold needs a gxformat2 `format` value for a `data` input, collection element, or workflow output. [[nextflow-params-to-galaxy-inputs]] decides whether something is a dataset or collection; this note only decides datatype extension and confidence.
Evidence quality:
- **Corpus-observed** claims cite pinned fixtures under `$NEXTFLOW_FIXTURES`, the shared clone at `/Users/jxc755/projects/repositories/workflow-fixtures/pipelines/`.
- **Foundry-internal*
...Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.
references/notes/nextflow-to-galaxy-channel-shape-mapping.mdcontent/research/nextflow-to-galaxy-channel-shape-mapping/index.md---
type: research
title: "Nextflow-to-Galaxy channel shape mapping"
tags:
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-06
revision: 2
related_notes:
- "[[nextflow-workflow-io-semantics]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-path-glob-to-galaxy-datatype]]"
- "[[galaxy-collection-semantics]]"
- "[[galaxy-collection-tools]]"
- "[[galaxy-apply-rules-dsl]]"
- "[[iwc-transformations-survey]]"
- "[[nextflow-operators-to-galaxy-collection-recipes]]"
- "[[galaxy-data-flow-draft-contract]]"
- "[[iwc-conditionals-survey]]"
- "[[manifest-to-mapped-collection-lifecycle]]"
- "[[map-workflow-enum-to-tool-parameter]]"
- "[[regex-relabel-via-tabular]]"
- "[[relabel-via-rules-and-find-replace]]"
- "[[reshape-relabel-remap-by-collection-axis]]"
- "[[sync-collections-by-identifier]]"
- "[[tabular-compute-new-column]]"
- "[[tabular-concatenate-collection-to-table]]"
- "[[tabular-cut-and-reorder-columns]]"
- "[[tabular-filter-by-column-value]]"
- "[[tabular-filter-by-regex]]"
- "[[tabular-group-and-aggregate-with-datamash]]"
- "[[tabular-join-on-key]]"
- "[[tabular-pivot-collection-to-wide]]"
- "[[tabular-prepend-header]]"
- "[[tabular-relabel-by-row-counter]]"
- "[[tabular-split-taxonomy-string]]"
- "[[tabular-sql-query]]"
- "[[tabular-synthesize-bed-from-3col]]"
- "[[tabular-to-collection-by-row]]"
- "[[iwc-map-over-lifecycle-survey]]"
- "[[nextflow-patterns]]"
related_molds:
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[implement-galaxy-tool-step]]"
sources:
- "https://github.com/galaxyproject/foundry/issues/52"
summary: "Maps common Nextflow channel, tuple, and
...Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the pipeline leaves open — a params entry with no Galaxy input, an emitted-but-unpublished output, a channel shape no collection maps cleanly onto.
references/notes/open-requirements-ledger.mdcontent/research/open-requirements-ledger/index.md---
type: research
title: "Open-requirements ledger"
tags:
- target/galaxy
status: draft
created: 2026-06-16
revised: 2026-08-29
revision: 3
related_notes:
- "[[galaxy-workflow-draft-format]]"
related_molds:
- "[[advance-galaxy-draft-step]]"
- "[[repair-galaxy-draft-topology]]"
- "[[implement-galaxy-tool-step]]"
summary: "Carried unresolved-requirements artifact the source→Galaxy pipeline discharges or explicitly surrenders, autonomously."
---
# Open-requirements ledger
The `open-requirements-ledger` is a single artifact threaded through the source→Galaxy pipeline that records **obligations the pipeline has taken on but not yet met** — a declared output with no producer, a parameter whose value the source never pinned, a tool with no corpus exemplar — and **source work it decided not to carry**. Each Mold that surfaces one **appends** it; each Mold whose decision closes one **marks it resolved**; the terminal path **surrenders** whatever remains open, explicitly, into the final artifact.
## Framing: obligations the pipeline discharges, not questions a human answers
This is deliberately *not* an "open questions for the user" list. The pipeline is autonomous — no human-in-the-loop gate is assumed. The ledger's consumers are **Molds and the loop's convergence gate**, with human readout a secondary affordance. An entry is closed by a downstream Mold doing work (wiring a producer, picking a wrapper, settling a value), or — when nothing can close it — surrendered: written into the final draft as a known, labelled gap rather than silently dropped or fabricated around.
The distinction matters because a "questions for a human" framing leaks an operator's personal interaction style into a tool meant to run inside anyone's harness. The ledger must behave identically
...Read source-level channel, parameter, process, and test-fixture evidence before choosing Galaxy 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
...Pick the right sample_sheet variant and translate nf-schema column metadata into Galaxy column_definitions when the source pipeline uses sample-sheet-shaped inputs.
Trigger: When the Nextflow summary reports a samplesheetToList materialization, a parameter whose nf-schema entry sets schema: assets/schema_*.json, or a channel built from splitCsv(header: true) over a tabular params input.
references/notes/galaxy-sample-sheet-collections.mdcontent/research/galaxy-sample-sheet-collections/index.md---
type: research
title: "Galaxy sample_sheet collection types"
tags:
- target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
related_notes:
- "[[galaxy-collection-semantics]]"
- "[[galaxy-collection-tools]]"
- "[[nextflow-workflow-io-semantics]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-path-glob-to-galaxy-datatype]]"
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[nextflow-to-galaxy-reference-data-mapping]]"
related_molds:
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
- "Galaxy PR #19305 (Implement Sample Sheets), merged 2025-07-30"
- "lib/galaxy/model/dataset_collections/types/sample_sheet.py"
- "lib/galaxy/model/dataset_collections/types/sample_sheet_util.py"
- "lib/galaxy/model/dataset_collections/type_description.py"
- "lib/galaxy/schema/schema.py (SampleSheetColumnDefinition, SampleSheetRow)"
- "lib/galaxy/tools/wrappers.py (DatasetCollectionWrapper.sample_sheet_row)"
- "lib/galaxy/tools/sample_sheet_to_tabular.xml"
- "lib/galaxy/webapps/galaxy/api/dataset_collections.py (sample_sheet_workbook endpoints)"
- "lib/galaxy/model/migrations/alembic/versions_gxy/3af58c192752_implement_sample_sheets.py"
summary: "Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist."
---
# Galaxy sample_sheet collection types
Reference for the Galaxy backend shape that targets structured per-row metadata — the natural landing zone for Nextflow `samplesheetToList` parameters and for any source-side idiom that pairs typed metadata columns with dataset references.
## Shape
A `sample_sheet` is a list-shaped collection where each element carries a typed `columns` row, and the parent collectio
...Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address.
Trigger: When deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.
references/notes/galaxy-workflow-testability-design.mdcontent/research/galaxy-workflow-testability-design/index.md---
type: research
tags:
- target/galaxy
status: draft
created: 2026-05-03
revised: 2026-05-06
revision: 2
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 requiring sibling `-tests.yml` updates.
- Prefer stable doma
...Cross-check source-side reference-data classifications before translating the reference-data brief into Galaxy workflow inputs.
Trigger: When the reference-data brief is silent, low-confidence, or conflicts with source evidence for iGenomes-derived params, coordinated bundles, compute-if-missing branches, multi-DB pick-lists, or cohort-specific assets.
references/notes/nextflow-reference-data-classification.mdcontent/research/nextflow-reference-data-classification/index.md---
type: research
title: "Nextflow reference-data classification"
tags:
- source/nextflow
status: draft
created: 2026-05-10
revised: 2026-05-10
revision: 3
related_notes:
- "[[summary-nextflow]]"
- "[[nextflow-to-galaxy-reference-data-mapping]]"
- "[[nextflow-summary-to-galaxy-reference-data]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
related_molds:
- "[[summarize-nextflow]]"
- "[[nextflow-summary-to-galaxy-reference-data]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
sources:
- "https://nf-co.re/docs/usage/reference_genomes"
- "https://github.com/nf-core/sarek/blob/master/conf/igenomes.config"
- "https://github.com/nf-core/configs"
- "https://github.com/galaxyproject/foundry/issues/221"
summary: "Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact."
---
# Nextflow reference-data classification
Reference-data shape varies along several roughly orthogonal dimensions: whether the pipeline consumes or produces reference data, the cardinality of the assets, whether they're keyed or per-asset, whether rebuild fallback exists, and whether multiple bundles run in parallel. The classifications below are flags an LLM can detect from a `summary-nextflow` artifact; a single pipeline often matches more than one. Grounded in the complexity bridge fixtures from galaxyproject/foundry#221.
For the Galaxy-side translation of these classifications, see [[nextflow-to-galaxy-reference-data-mapping]].
## None
Pipeline consumes no reference data. Detection: `params[]` has no path-shaped referen
...Translate iGenomes-style and per-asset reference-data params into Galaxy inputs without inheriting nf-core's reference-resolution magic; v1 posture is explicit optional inputs with in-tool rebuild on absence.
Trigger: When the source pipeline declares iGenomes-derived params (params.genome with getGenomeAttribute), per-asset reference path params (fasta, fasta_fai, dict, bwa_index, dbsnp, known_indels, intervals, pon), or any compute-if-missing index-building branch in the source.
references/notes/nextflow-to-galaxy-reference-data-mapping.mdcontent/research/nextflow-to-galaxy-reference-data-mapping/index.md---
type: research
title: "Nextflow to Galaxy reference-data mapping"
tags:
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-08
revised: 2026-05-10
revision: 5
related_notes:
- "[[nextflow-reference-data-classification]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-path-glob-to-galaxy-datatype]]"
- "[[summary-nextflow]]"
- "[[nextflow-summary-to-galaxy-reference-data]]"
- "[[nextflow-summary-to-galaxy-template]]"
- "[[galaxy-sample-sheet-collections]]"
- "[[galaxy-datatypes-conf]]"
related_molds:
- "[[summarize-nextflow]]"
- "[[nextflow-summary-to-galaxy-reference-data]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
- "[[nextflow-summary-to-galaxy-template]]"
sources:
- "https://github.com/galaxyproject/foundry/issues/221"
summary: "Galaxy-side translation of Nextflow reference-data classifications: idioms available, the v1 posture, datatype defaults, and the in-tool rebuild trade-off."
---
# Nextflow to Galaxy reference-data mapping
Mapping research for [[nextflow-summary-to-galaxy-reference-data]]. Once a Nextflow pipeline's reference-data usage is classified per [[nextflow-reference-data-classification]], this note pins the Galaxy-side translation: idioms available, the v1 posture, datatype defaults, the in-tool rebuild trade-off, and known representation gaps the brief should flag.
## Galaxy side
Galaxy has multiple idioms for surfacing reference data. The bullets below are presented as available shapes; the recommendations that follow narrow them to the v1 posture.
- **`dbkey`-keyed cached lookups.** Workflow inputs carry a `dbkey` annotation; tools consume an admin-pre-loaded data table indexed by `dbkey` (BWA indexes, GATK known-sites, dbSNP for common bui
...
# nextflow-summary-to-galaxy-interface
Follow the procedure below and use the artifact/reference sections as the runtime contract.
## When To Use
- Map a Nextflow summary into a Galaxy 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 interface choices.
- Read artifact `nextflow-galaxy-reference-data`. Produced by `nextflow-summary-to-galaxy-reference-data`. Reference-data shape brief from nextflow-summary-to-galaxy-reference-data that pins per-asset reference inputs and rebuild-on-absence behavior.
- Read artifact `open-requirements-ledger`. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `nextflow-summary-to-galaxy-data-flow`, `nextflow-summary-to-galaxy-interface`, `nextflow-summary-to-galaxy-reference-data`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. Carried obligations ledger open-requirements-ledger: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
## Outputs
- Write artifact `nextflow-galaxy-interface` as `nextflow-galaxy-interface.md`. Format: `markdown`. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance.
- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
## Required Tools
- None declared. Procedure should not assume external CLIs are present.
## Load Upfront
- `references/notes/nextflow-params-to-galaxy-inputs.md`: Research note copied verbatim into the bundle. Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.
- `references/notes/nextflow-path-glob-to-galaxy-datatype.md`: Research note copied verbatim into the bundle. Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.
- `references/notes/nextflow-to-galaxy-channel-shape-mapping.md`: Research note copied verbatim into the bundle. Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.
- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the pipeline leaves open — a params entry with no Galaxy input, an emitted-but-unpublished output, a channel shape no collection maps cleanly onto.
- `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 Galaxy workflow inputs and outputs.
## Load On Demand
- `references/notes/galaxy-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Pick the right sample_sheet variant and translate nf-schema column metadata into Galaxy column_definitions when the source pipeline uses sample-sheet-shaped inputs. Use when: the Nextflow summary reports a samplesheetToList materialization, a parameter whose nf-schema entry sets schema: assets/schema_*.json, or a channel built from splitCsv(header: true) over a tabular params input.
- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address. Use when: deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.
- `references/notes/nextflow-reference-data-classification.md`: Research note copied verbatim into the bundle. Cross-check source-side reference-data classifications before translating the reference-data brief into Galaxy workflow inputs. Use when: the reference-data brief is silent, low-confidence, or conflicts with source evidence for iGenomes-derived params, coordinated bundles, compute-if-missing branches, multi-DB pick-lists, or cohort-specific assets.
- `references/notes/nextflow-to-galaxy-reference-data-mapping.md`: Research note copied verbatim into the bundle. Translate iGenomes-style and per-asset reference-data params into Galaxy inputs without inheriting nf-core's reference-resolution magic; v1 posture is explicit optional inputs with in-tool rebuild on absence. Use when: the source pipeline declares iGenomes-derived params (params.genome with getGenomeAttribute), per-asset reference path params (fasta, fasta_fai, dict, bwa_index, dbsnp, known_indels, intervals, pon), or any compute-if-missing index-building branch in the source.
## Validation
- None declared.
## Procedure
Read a Nextflow summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Capture workflow inputs, workflow outputs, labels, Galaxy collection shapes, checkpoint outputs worth exposing for tests, source-summary provenance, confidence, and open questions.
The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by nextflow-summary-to-galaxy-data-flow, nextflow-summary-to-galaxy-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.