Agent Skill · cast

nextflow-summary-to-galaxy-data-flow

Translate a Nextflow summary into a Galaxy data-flow design brief.

Install with Claude Code

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

Then invoke as:

/foundry-skills:nextflow-summary-to-galaxy-data-flow

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-summary-to-galaxy-data-flow

Skill Bundle

/ packaged cast

attached files: 14
upfront: 5
on demand: 9
cast rev: 3
validated: 0

Produces: 2 artifacts.

Consumes: 4 artifacts.

Artifact Contract

/ skill handoff

Produces

nextflow-galaxy-data-flow

Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, Galaxy tool needs, confidence, open questions.

markdownnextflow-galaxy-data-flow.md

Raw artifact contract

{
  "id": "nextflow-galaxy-data-flow",
  "kind": "markdown",
  "default_filename": "nextflow-galaxy-data-flow.md",
  "description": "Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, Galaxy tool needs, confidence, open questions."
}

open-requirements-ledger

Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.

yamlopen-requirements.ledger.yml

Raw artifact contract

{
  "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."
}

Consumes

summary-nextflow

Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the JSON the data-flow translation reads.

Raw artifact contract

{
  "id": "summary-nextflow",
  "description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the JSON the data-flow translation reads.",
  "inherited_schema": "[[summary-nextflow]]",
  "producers": [
    "summarize-nextflow"
  ]
}

nextflow-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.

Raw artifact contract

{
  "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"
  ]
}

nextflow-galaxy-interface

Preceding Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.

Raw artifact contract

{
  "id": "nextflow-galaxy-interface",
  "description": "Preceding Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.",
  "producers": [
    "nextflow-summary-to-galaxy-interface"
  ]
}

open-requirements-ledger

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.

Raw artifact contract

{
  "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"
  ]
}

Attached Files

/ runtime references

Load upfront

research

galaxy-data-flow-draft-contract

packaged

Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.

upfront runtime verbatim hypothesis deterministic 7.3 KB

bundle: references/notes/galaxy-data-flow-draft-contract.md
source: content/research/galaxy-data-flow-draft-contract/index.md

Preview md

---
type: research
title: "Galaxy data-flow draft contract"
tags:
  - target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-03
revision: 2
related_notes:
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-operators-to-galaxy-collection-recipes]]"
  - "[[galaxy-workflow-draft]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[freeform-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
  - "[[advance-galaxy-draft-step]]"
sources:
  - "https://github.com/galaxyproject/foundry/issues/54"
summary: "Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation."
---

# Galaxy Data-Flow Draft Contract

This is an architectural contract, not a schema. Evidence is strongest for Mold and Pipeline boundaries. Proposed fields are speculative until exercised by two or three worked translations.

## Boundary

The data-flow draft owns a target-shaped abstract DAG for Galaxy. It should not be valid `gxformat2` and should not resolve exact Tool Shed tools.

Data-flow draft owns:

- Galaxy-facing workflow inputs and outputs.
- Abstract nodes, edges, branches, collection mapping, collection reduction, and placeholder transformations.
- Input/output shape decisions such as `File`, `list`, `paired`, `list:paired`, or `list:list`.
- Conceptual Galaxy idioms: map-over, reduction, Apply Rules, collection cleanup, identifier synchronization, tabular bridge, fan-in / combine (concatenate, merge, or union N sources into one — a distinct node, not a side-effect of a reshape).
- Abstract unresolved tool nee
...

research

nextflow-operators-to-galaxy-collection-recipes

packaged

Classify Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.

upfront runtime verbatim corpus-observed deterministic 6.4 KB

bundle: references/notes/nextflow-operators-to-galaxy-collection-recipes.md
source: content/research/nextflow-operators-to-galaxy-collection-recipes/index.md

Preview md

---
type: research
title: "Nextflow operators to Galaxy collection recipes"
tags:
  - source/nextflow
  - target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
related_notes:
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[galaxy-collection-semantics]]"
  - "[[galaxy-collection-tools]]"
  - "[[galaxy-apply-rules-dsl]]"
  - "[[iwc-transformations-survey]]"
  - "[[iwc-tabular-operations-survey]]"
  - "[[galaxy-data-flow-draft-contract]]"
  - "[[iwc-map-over-lifecycle-survey]]"
  - "[[nextflow-patterns]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[implement-galaxy-tool-step]]"
  - "[[debug-galaxy-workflow-output]]"
sources:
  - "https://github.com/galaxyproject/foundry/issues/53"
summary: "Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers."
---

# Nextflow Operators To Galaxy Collection Recipes

Most Nextflow operators are not Galaxy tools. Translate them first as source-side data-flow intent, then decide whether the Galaxy representation is simple wiring, collection semantics, an explicit Galaxy step, or a user-review checkpoint.

## Decision Vocabulary

| Label | Meaning |
|---|---|
| `channel-only rewiring` | The operator disappears into Galaxy connections, labels, branch wiring, or output selection. |
| `Galaxy collection semantics` | Translation relies on collection identifiers, collection type, map-over, reduction, or nesting behavior. |
| `explicit Galaxy step` | Add a collection-operation, tabular, text-processing, or domain tool step. |
| `user review` | Translation is likely lossy or semantically ambiguous. |

## Operator Recipes

| Nextflow operator | Galaxy recipe | Class | Confidence |
|---|---|---|---|
| `map` | Treat metadata-only proje
...

research

nextflow-to-galaxy-channel-shape-mapping

packaged

Translate Nextflow channel, tuple, and path shapes into Galaxy dataset and collection shapes.

upfront runtime verbatim corpus-observed deterministic 8.5 KB

bundle: references/notes/nextflow-to-galaxy-channel-shape-mapping.md
source: content/research/nextflow-to-galaxy-channel-shape-mapping/index.md

Preview 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
...

research

open-requirements-ledger

packaged

Inherit open entries rather than re-deriving them, close the ones this brief's wiring and collection decisions settle, and append data-flow obligations the channel topology leaves open — an operator with no Galaxy collection recipe, a value channel with no Galaxy carrier, a join whose key Galaxy can't reconstruct.

upfront runtime verbatim hypothesis deterministic 15.5 KB

bundle: references/notes/open-requirements-ledger.md
source: content/research/open-requirements-ledger/index.md

Preview 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
...

schema

summary-nextflow

packaged

Read process, channel, operator, and fixture structure while drafting Galaxy-facing abstract data flow.

upfront runtime verbatim corpus-observed deterministic 59.2 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
...

Load on demand

pattern

galaxy-collection-patterns

packaged

Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.

Trigger: When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.

on-demand runtime verbatim corpus-observed deterministic 4.6 KB

bundle: references/patterns/galaxy-collection-patterns.md
source: content/patterns/galaxy-collection-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: collection patterns"
aliases:
  - "Galaxy collection pattern MOC"
  - "collection transformation patterns"
  - "IWC collection pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/collection-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
summary: "Use this MOC to choose corpus-grounded Galaxy collection transformation patterns."
related_notes:
  - "[[iwc-transformations-survey]]"
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[manifest-to-mapped-collection-lifecycle]]"
  - "[[cleanup-sync-and-publish-nonempty-results]]"
  - "[[reshape-relabel-remap-by-collection-axis]]"
  - "[[fan-in-bundle-consume-and-flatten]]"
  - "[[collection-cleanup-after-mapover-failure]]"
  - "[[sync-collections-by-identifier]]"
  - "[[harmonize-by-sortlist-from-identifiers]]"
  - "[[regex-relabel-via-tabular]]"
  - "[[relabel-via-rules-and-find-replace]]"
  - "[[collection-swap-nesting-with-apply-rules]]"
  - "[[collection-split-identifier-via-rules]]"
  - "[[collection-build-list-paired-with-apply-rules]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: collection patterns

This is the runtime-facing map for Galaxy collection transformation choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation and recipe pag
...

pattern

galaxy-conditionals-patterns

packaged

Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns.

Trigger: When data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.

on-demand runtime verbatim corpus-observed deterministic 2.6 KB

bundle: references/patterns/galaxy-conditionals-patterns.md
source: content/patterns/galaxy-conditionals-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: conditionals patterns"
aliases:
  - "Galaxy conditional pattern MOC"
  - "Galaxy when patterns"
  - "conditional workflow patterns"
tags:
  - target/galaxy
  - topic/galaxy-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
summary: "Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns."
related_notes:
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[conditional-run-optional-step]]"
  - "[[conditional-route-between-alternative-outputs]]"
  - "[[conditional-gate-on-nonempty-result]]"
  - "[[conditional-transform-or-pass-through]]"
  - "[[collection-cleanup-after-mapover-failure]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: conditionals patterns

This is the runtime-facing map for Galaxy conditional workflow choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation and recipe pages are the actionable references.

## Direct Gates

- [[conditional-run-optional-step]] — expose or derive a boolean, connect it as `inputs.when`, and use `when: $(inputs.when)` to skip optional steps.
- [[conditional-gate-on-nonempty-result]] — compute a boolean from empty/non-empty dataset or collection state before gating downstream reporting/export. The MGnify recipe is corpus-backed but clunky pending verified-pattern workflow work.

## Routes and Fallbacks

- [[conditional-route-between-alternative-outputs]] — run one of sever
...

pattern

galaxy-interval-patterns

packaged

Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes.

Trigger: When the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.

on-demand runtime verbatim corpus-observed deterministic 5.5 KB

bundle: references/patterns/galaxy-interval-patterns.md
source: content/patterns/galaxy-interval-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: genomic interval patterns"
aliases:
  - "Galaxy interval pattern MOC"
  - "genomic interval transformation patterns"
  - "IWC interval pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/interval-transform
status: draft
created: 2026-06-10
revised: 2026-08-03
revision: 2
summary: "Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features."
related_notes:
  - "[[iwc-interval-operations-survey]]"
related_patterns:
  - "[[interval-overlap-filter]]"
  - "[[interval-coverage]]"
  - "[[interval-merge-overlapping]]"
  - "[[interval-window-flank]]"
  - "[[interval-consensus-by-multi-intersect]]"
  - "[[interval-mask-by-set-algebra]]"
  - "[[interval-windowed-coverage]]"
  - "[[tabular-synthesize-bed-from-3col]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: genomic interval patterns

The runtime-facing map for Galaxy **coordinate-feature** choices — operations that understand `chrom/start/end/strand`, as opposed to opaque-column [[galaxy-tabular-patterns]] or container-shaped [[galaxy-collection-patterns]]. Use it before loading raw survey notes; [[iwc-interval-operations-survey]] is the evidence backing, these pages are the actionable references.

This is the smallest of the three data-shape MOCs by design. Interval algebra is a real but moderate cluster in IWC — concentrated in epigenetics peak-consensus and SARS-CoV-2 masking — and its highest-value 
...

pattern

galaxy-tabular-patterns

packaged

Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns.

Trigger: When data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.

on-demand runtime verbatim corpus-observed deterministic 3.3 KB

bundle: references/patterns/galaxy-tabular-patterns.md
source: content/patterns/galaxy-tabular-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: tabular patterns"
aliases:
  - "Galaxy tabular pattern MOC"
  - "tabular transformation patterns"
  - "IWC tabular pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/tabular-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
summary: "Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns."
related_notes:
  - "[[iwc-tabular-operations-survey]]"
related_patterns:
  - "[[tabular-filter-by-column-value]]"
  - "[[tabular-filter-by-regex]]"
  - "[[tabular-cut-and-reorder-columns]]"
  - "[[tabular-compute-new-column]]"
  - "[[tabular-join-on-key]]"
  - "[[tabular-group-and-aggregate-with-datamash]]"
  - "[[tabular-sql-query]]"
  - "[[tabular-prepend-header]]"
  - "[[tabular-synthesize-bed-from-3col]]"
  - "[[tabular-split-taxonomy-string]]"
  - "[[tabular-relabel-by-row-counter]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: tabular patterns

This is the runtime-facing map for Galaxy tabular transformation choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation pages are the actionable references.

## Row And Column Operations

- [[tabular-filter-by-column-value]] — keep/drop rows by string column value with `Filter1`.
- [[tabular-filter-by-regex]] — keep/drop rows by regex or pa
...

research

galaxy-sample-sheet-collections

packaged

Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it.

Trigger: When the upstream interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or when the Nextflow summary shows tuple(meta, path...) channel shape originating from samplesheetToList or splitCsv(header: true).

on-demand runtime verbatim corpus-observed deterministic 8.4 KB

bundle: references/notes/galaxy-sample-sheet-collections.md
source: content/research/galaxy-sample-sheet-collections/index.md

Preview 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
...

research

nextflow-conditional-to-galaxy-subworkflow-when

packaged

Decide between subworkflow `when:` and inline tool-step `when:` for each source conditional, and pick the right output fan-in primitive (`pick_value` vs twin-cascade) so the data-flow brief carries a coherent conditional disposition forward.

Trigger: When the Nextflow summary's `workflow.conditionals[]` is non-empty, or when subworkflow boundaries in the source align with parameter-driven branches (step, aligner, wes, tools, skip_*, use_*).

on-demand runtime verbatim corpus-observed deterministic 13.6 KB

bundle: references/notes/nextflow-conditional-to-galaxy-subworkflow-when.md
source: content/research/nextflow-conditional-to-galaxy-subworkflow-when/index.md

Preview md

---
type: research
title: "Nextflow conditional to Galaxy subworkflow / when"
tags:
  - source/nextflow
  - target/galaxy
status: draft
created: 2026-05-08
revised: 2026-05-08
revision: 1
related_notes:
  - "[[nextflow-to-galaxy-reference-data-mapping]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[summary-nextflow]]"
  - "[[gxformat2-schema]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
sources:
  - "https://github.com/galaxyproject/gxformat2"
  - "https://github.com/iwc-workflows"
summary: "Stub. Translate Nextflow conditionals into Galaxy `when:` (single-workflow v1). Subworkflow vs inline is an aesthetic call, not a rule."
---

# Nextflow conditional to Galaxy subworkflow / when

Stub. Surfaced from sarek emulation (2026-05-08). Companion to [[nextflow-to-galaxy-reference-data-mapping]] — same v1 posture (one Galaxy workflow per source pipeline; trench-coat shape is acceptable as a draft for human review), different gap (control flow rather than reference data).

## Posture

For v1 of the Nextflow-to-Galaxy translation Molds the output is a single Galaxy workflow per source pipeline, even when the source has substantial branching. IWC reviewers historically prefer sibling workflows for what looks like one pipeline with toggles, and we agree; but for the *translation step* a single artifact keeps the Mold pipeline deterministic, the harness simple, and the reviewer's mental model of "this draft maps 1:1 to the source" intact. Sibling-extraction is a polish pass a human or follow-up Mold runs *after* translation, not a decision the translation Mold makes.

The question this note addresses is: given that v1 is one Galaxy workflow, *how* should source conditionals translate? The two structural 
...

research

nextflow-path-glob-to-galaxy-datatype

packaged

Preserve datatype confidence while translating path-like data-flow edges, process output patterns, and published outputs.

Trigger: When choosing or reviewing Galaxy datatype extensions for data-flow edges, collection elements, or output datasets.

on-demand runtime verbatim corpus-observed deterministic 12.8 KB

bundle: references/notes/nextflow-path-glob-to-galaxy-datatype.md
source: content/research/nextflow-path-glob-to-galaxy-datatype/index.md

Preview 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*
...

research

nextflow-reference-data-classification

packaged

Cross-check source-side reference-data classifications before deciding how reference assets and optional rebuild branches flow through the Galaxy data-flow draft.

Trigger: When the reference-data or interface 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.

on-demand runtime verbatim corpus-observed deterministic 7.9 KB

bundle: references/notes/nextflow-reference-data-classification.md
source: content/research/nextflow-reference-data-classification/index.md

Preview 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
...

research

nextflow-to-galaxy-reference-data-mapping

packaged

Decide how reference assets and their indexes flow through the Galaxy data-flow draft (preserving dbkey through map-overs, deferring index-building to wrappers vs surfacing as workflow steps).

Trigger: When the upstream interface brief carries reference-data inputs (FASTA, fai, dict, indexes, known sites, intervals, PoN) or when the source pipeline's compute-if-missing branches imply rebuild semantics the data flow has to honor.

on-demand runtime verbatim corpus-observed deterministic 12.3 KB

bundle: references/notes/nextflow-to-galaxy-reference-data-mapping.md
source: content/research/nextflow-to-galaxy-reference-data-mapping/index.md

Preview 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
...

SKILL.md


# nextflow-summary-to-galaxy-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 Galaxy data-flow design brief.

## Inputs

- Read artifact `summary-nextflow`. Schema: summary-nextflow. Produced by `summarize-nextflow`. Structured Nextflow pipeline summary emitted by summarize-nextflow; the JSON the data-flow translation reads.
- 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 `nextflow-galaxy-interface`. Produced by `nextflow-summary-to-galaxy-interface`. Preceding Galaxy interface brief from nextflow-summary-to-galaxy-interface that pins inputs, outputs, and labels.
- 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-data-flow` as `nextflow-galaxy-data-flow.md`. Format: `markdown`. Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, Galaxy tool needs, confidence, open questions.
- 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/galaxy-data-flow-draft-contract.md`: Research note copied verbatim into the bundle. Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
- `references/notes/nextflow-operators-to-galaxy-collection-recipes.md`: Research note copied verbatim into the bundle. Classify Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
- `references/notes/nextflow-to-galaxy-channel-shape-mapping.md`: Research note copied verbatim into the bundle. Translate Nextflow channel, tuple, and path shapes into Galaxy dataset and collection 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 wiring and collection decisions settle, and append data-flow obligations the channel topology leaves open — an operator with no Galaxy collection recipe, a value channel with no Galaxy carrier, a join whose key Galaxy can't reconstruct.
- `references/schemas/summary-nextflow.schema.json`: Schema file copied verbatim into the bundle. Read process, channel, operator, and fixture structure while drafting Galaxy-facing abstract data flow.

## Load On Demand

- `references/patterns/galaxy-collection-patterns.md`: Pattern note copied verbatim into the bundle. Ground collection-shape choices in curated, corpus-observed operation and recipe patterns. Use when: selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.
- `references/patterns/galaxy-conditionals-patterns.md`: Pattern note copied verbatim into the bundle. Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns. Use when: data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
- `references/patterns/galaxy-interval-patterns.md`: Pattern note copied verbatim into the bundle. Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes. Use when: the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
- `references/patterns/galaxy-tabular-patterns.md`: Pattern note copied verbatim into the bundle. Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns. Use when: data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.
- `references/notes/galaxy-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it. Use when: the upstream interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or when the Nextflow summary shows tuple(meta, path...) channel shape originating from samplesheetToList or splitCsv(header: true).
- `references/notes/nextflow-conditional-to-galaxy-subworkflow-when.md`: Research note copied verbatim into the bundle. Decide between subworkflow `when:` and inline tool-step `when:` for each source conditional, and pick the right output fan-in primitive (`pick_value` vs twin-cascade) so the data-flow brief carries a coherent conditional disposition forward. Use when: the Nextflow summary's `workflow.conditionals[]` is non-empty, or when subworkflow boundaries in the source align with parameter-driven branches (step, aligner, wes, tools, skip_*, use_*).
- `references/notes/nextflow-path-glob-to-galaxy-datatype.md`: Research note copied verbatim into the bundle. Preserve datatype confidence while translating path-like data-flow edges, process output patterns, and published outputs. Use when: choosing or reviewing Galaxy datatype extensions for data-flow edges, collection elements, or output datasets.
- `references/notes/nextflow-reference-data-classification.md`: Research note copied verbatim into the bundle. Cross-check source-side reference-data classifications before deciding how reference assets and optional rebuild branches flow through the Galaxy data-flow draft. Use when: the reference-data or interface 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. Decide how reference assets and their indexes flow through the Galaxy data-flow draft (preserving dbkey through map-overs, deferring index-building to wrappers vs surfacing as workflow steps). Use when: the upstream interface brief carries reference-data inputs (FASTA, fai, dict, indexes, known sites, intervals, PoN) or when the source pipeline's compute-if-missing branches imply rebuild semantics the data flow has to honor.

## Validation

- None declared.

## Procedure

Read a Nextflow summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, Galaxy tool needs, confidence, and open questions.

The output is not gxformat2 and should not resolve exact Tool Shed tools. Nor does it rule them out. Recording that a step's tool does not exist, will not be found, or must be authored is the same adjudication made negative, and it belongs to advance-galaxy-draft-step, which owns routing. Say what each step needs a tool to *do*; let discovery report what exists. Justify step granularity from the source's own structure — subworkflow boundaries, the ratio of plumbing to scientific work. A guess about tool availability is not a justification.

## 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.