Structured contract copied for validation or lookup.
- Purpose
- Read source-level channel, parameter, process, and test-fixture evidence before choosing Galaxy workflow inputs and outputs.
nextflow-summary-to-galaxy-interface
Map a Nextflow summary into a Galaxy workflow interface design brief.
Mold health
ok- Source layout
Directory Mold with only index.md frontmatter.
- Axis fields
source-specific fields are coherent.
- Eval plan
eval.md declares cases and check type.
- Typed refs
8 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Artifact handoffs
/ pipeline contractProduces
-
Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance.
Consumes
-
Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source-of-truth JSON for interface choices.
-
Reference-data shape brief from [[nextflow-summary-to-galaxy-reference-data]] that pins per-asset reference inputs and rebuild-on-absence behavior.
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.
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.