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nextflow-summary-to-galaxy-interface

Map a Nextflow summary into a Galaxy workflow interface design brief.

Related: summary-nextflow
nextflow-summary-to-galaxy-template
nextflow-reference-data-classification
nextflow-params-to-galaxy-inputs
nextflow-path-glob-to-galaxy-datatype

Mold health

Source layout
Directory Mold with only index.md frontmatter.
Axis fields
source-specific fields are coherent.
Eval plan
Abstract oracle: fixture-independent property checks any run must satisfy.

eval.md declares properties and check type.
eval.md ↗
Scenarios
Concrete cases: fixtures bound to expected values, run against the eval properties.

scenarios.md declares cases bound to fixtures.
scenarios.md ↗
Typed refs
9 typed references; 0 resolver issues.
On-demand triggers
All on-demand references describe triggers.
Evidence checks
Hypothesis references include verification.

axis: source-specific
source: nextflow
name: nextflow-summary-to-galaxy-interface

contract

Reference Loading

Typed Mold references describe what casting consumes and when the generated skill should load each artifact.

Researchopen-requirements-ledger

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Hypothesis

Purpose: Carry the open-requirements ledger: read open entries bearing on this step's decisions, mark resolved the ones it closes, and append any new unmet need it surfaces.
Verify: Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.

Schemasummary-nextflow

Structured contract copied for validation or lookup.

Runtime Upfront Verbatim Corpus Observed

Purpose: Read source-level channel, parameter, process, and test-fixture evidence before choosing Galaxy workflow inputs and outputs.

Researchnextflow-params-to-galaxy-inputs

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Corpus Observed

Purpose: Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.

Researchnextflow-path-glob-to-galaxy-datatype

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Corpus Observed

Purpose: Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.

Researchnextflow-to-galaxy-channel-shape-mapping

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Corpus Observed

Purpose: Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.

Researchgalaxy-workflow-testability-design

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Researchgalaxy-sample-sheet-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Researchnextflow-reference-data-classification

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Researchnextflow-to-galaxy-reference-data-mapping

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Cast artifacts

Claude skillnextflow-summary-to-galaxy-interface— Map a Nextflow summary into a Galaxy workflow interface design brief.

How to install →

Artifact handoffs

/ pipeline contract

Produces

nextflow-galaxy-interface markdown nextflow-galaxy-interface.md

Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance.
consumed by
open-requirements-ledger yaml open-requirements.ledger.yml

Updated obligations ledger: new unmet needs this step surfaces appended; prior entries its decisions close marked resolved.
consumed by

Consumes

summary-nextflow

Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for interface choices.
produced by
- 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.
produced by
- nextflow-summary-to-galaxy-reference-data
open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; this design step appends new unmet needs and marks ones its decisions resolve.
produced by

nextflow-summary-to-galaxy-interface

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.

Carry the open-requirements-ledger through this step: read the open entries that bear on the choices you make here, mark resolved any your decisions close, and append any new unmet need you surface — a declared output with no producer, an unpinned parameter, a tool with no corpus exemplar — so a later Mold inherits it instead of re-deriving it.

Incoming References (17)

nextflow-summary-to-galaxy-data-flowrelated note— Translate a Nextflow summary into a Galaxy data-flow design brief.
nextflow-summary-to-galaxy-reference-datarelated mold— Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
nextflow-summary-to-galaxy-templaterelated note— gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
Galaxy paired_or_unpaired collection typerelated mold— Galaxy's `paired_or_unpaired` collection type: discriminated-union shape for paired-or-single reads, no workflow-level mode switch needed. Galaxy PR #19377.
Galaxy sample_sheet collection typesrelated mold— Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist.
Nextflow params to Galaxy workflow inputsrelated note— Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs.
Nextflow params to Galaxy workflow inputsrelated mold— Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs.
Nextflow path/glob to Galaxy datatype mappingrelated note— Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions.
Nextflow path/glob to Galaxy datatype mappingrelated mold— Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions.
Nextflow reference-data classificationrelated note— Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact.
Nextflow reference-data classificationrelated mold— Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact.
Nextflow-to-Galaxy channel shape mappingrelated mold— Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes.
Nextflow to Galaxy reference-data mappingrelated mold— Galaxy-side translation of Nextflow reference-data classifications: idioms available, the v1 posture, datatype defaults, and the in-tool rebuild trade-off.
Nextflow workflow I/O semanticsrelated mold— Defines Nextflow workflow inputs and outputs from docs plus observed fixture pipeline structures.
nf-schema sample sheet validation gaps in Galaxyrelated mold— nf-schema validation mapped to Galaxy column_definitions: what survives, degrades, or is lost; Galaxy work items + cast loss-recording vocabulary.
Nextflow pipeline summaryrelated note— JSON Schema for the structured summary emitted by the summarize-nextflow Mold.