Map a Nextflow summary into a Galaxy workflow interface design brief.
/plugin marketplace add jmchilton/foundry
/plugin install foundry-skills@galaxy-workflow-foundryThen invoke as:
/foundry-skills:nextflow-summary-to-galaxy-interfaceProduces: 1 artifact.
Consumes: 2 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."
}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"
]
}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.md---
type: research
subtype: component
title: "Nextflow params to Galaxy workflow inputs"
tags:
- research/component
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-08
revision: 4
ai_generated: true
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 `$NEXTFLOW_FIXTURES`, the shared cl
...Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.
references/notes/nextflow-path-glob-to-galaxy-datatype.mdcontent/research/nextflow-path-glob-to-galaxy-datatype.md---
type: research
subtype: component
title: "Nextflow path/glob to Galaxy datatype mapping"
tags:
- research/component
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-06
revision: 1
ai_generated: true
related_notes:
- "[[nextflow-workflow-io-semantics]]"
- "[[gxformat2-workflow-inputs]]"
- "[[galaxy-datatypes-conf]]"
- "[[galaxy-sample-sheet-collections]]"
- "[[nextflow-params-to-galaxy-inputs]]"
- "[[nextflow-to-galaxy-channel-shape-mapping]]"
- "[[summary-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
related_molds:
- "[[summarize-nextflow]]"
- "[[nextflow-summary-to-galaxy-interface]]"
- "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
- "content/research/datatypes_conf.xml.sample"
- "https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/config/datatypes_conf.xml.sample"
- "https://www.nextflow.io/docs/latest/process.html"
- "https://www.nextflow.io/docs/latest/reference/channel.html"
- "https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/"
summary: "Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions."
---
# Nextflow path/glob to Galaxy datatype mapping
Use this note when a Nextflow-to-Galaxy Mold needs a gxformat2 `format` value for a `data` input, collection element, or workflow output. [[nextflow-params-to-galaxy-inputs]] decides whether something is a dataset or collection; this note only decides datatype extension and confidence.
Evidence quality:
- **Corpus-observed** claims cite pinned fixtures under `$NEXTFLOW_FIXTURES`, the shared clone at `/Users/jxc755/projects/repositories/workflow-fixt
...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.md---
type: research
subtype: component
title: "Nextflow-to-Galaxy channel shape mapping"
tags:
- research/component
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-06
revision: 2
ai_generated: true
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/jmchilton/foundry/issu
...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",
"$comment": "Canonical source: packages/summarize-nextflow/src/schema/summary-nextflow.schema.json in jmchilton/foundry. Mold frontmatter cites this schema via [[summary-nextflow]] wiki-links; the cast pipeline imports the `summaryNextflowSchema` runtime export and serializes it into cast bundles.",
"title": "Nextflow Pipeline Summary",
"description": "Structured per-source summary emitted by the summarize-nextflow Mold.\n\nPer-source schema by design — paper, Nextflow, and CWL each have their own summary shape; downstream Molds (data flow, templates, tool wrappers) consume any source's summary and handle the polymorphism.\n\nField names mirror gxy-sketches' SketchSource / ToolSpec / TestDataRef / ExpectedOutputRef where parity exists; see content/research/gxy-sketches-alignment.md.",
"$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: true)` m
...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.md---
type: research
subtype: component
title: "Galaxy sample_sheet collection types"
tags:
- research/component
- target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
ai_generated: true
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 el
...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.md---
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
...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.md---
type: research
subtype: component
title: "Nextflow reference-data classification"
tags:
- research/component
- source/nextflow
status: draft
created: 2026-05-10
revised: 2026-05-10
revision: 3
ai_generated: true
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/jmchilton/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 jmchilton/foundry#221.
For the Galaxy-side translation of these classifications, see [[nextflow-to-galaxy-reference-data-mapping]].
## None
Pipeline consumes no reference d
...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.md---
type: research
subtype: component
title: "Nextflow to Galaxy reference-data mapping"
tags:
- research/component
- source/nextflow
- target/galaxy
status: draft
created: 2026-05-08
revised: 2026-05-10
revision: 5
ai_generated: true
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/jmchilton/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 `db
...
# 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.
## 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.
## 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/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.
## 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.