Home Mold

nextflow-summary-to-galaxy-data-flow

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

reviewed source/nextflow target/galaxy

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

Mold health

Source layout
Every file beside index.md is one the mold kind declares.
Axis fields
source-specific fields are coherent.
Eval plan
Abstract oracle: the properties any cast of this Mold must satisfy.

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

scenarios.md declares cases bound to fixtures.
scenarios.md ↗
Typed refs
14 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-data-flow

contract

Reference Loading

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

Research open-requirements-ledger

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Hypothesis

Purpose: 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.
Verify: Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.

Schema summary-nextflow

Structured contract copied for validation or lookup.

Runtime Upfront Verbatim Corpus Observed

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

Research galaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Hypothesis

Purpose: Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
Verify: Promote after two worked Galaxy translations preserve this Mold boundary without moving fields.

Research nextflow-to-galaxy-channel-shape-mapping

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Corpus Observed

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

Research nextflow-path-glob-to-galaxy-datatype

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Research nextflow-operators-to-galaxy-collection-recipes

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime Upfront Verbatim Corpus Observed

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

Pattern galaxy-collection-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.
Trigger: When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.

Pattern galaxy-tabular-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Pattern galaxy-conditionals-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Pattern galaxy-interval-patterns

Workflow-construction idiom. Copied verbatim.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Research galaxy-sample-sheet-collections

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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).

Research nextflow-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 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.

Research nextflow-to-galaxy-reference-data-mapping

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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.

Research nextflow-conditional-to-galaxy-subworkflow-when

Background synthesis loaded by explicit progressive-disclosure metadata.

Runtime On Demand Verbatim Corpus Observed

Purpose: 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_*).

Cast artifacts

Claude skill nextflow-summary-to-galaxy-data-flow — Translate a Nextflow summary into a Galaxy data-flow design brief.

How to install →

Artifact handoffs

/ pipeline contract

Produces

nextflow-galaxy-data-flow markdown nextflow-galaxy-data-flow.md

Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, Galaxy tool needs, confidence, open questions.
consumed by
- compare-against-iwc-exemplar
- nextflow-summary-to-galaxy-template
open-requirements-ledger yaml open-requirements.ledger.yml

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

Consumes

summary-nextflow

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

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

nextflow-summary-to-galaxy-data-flow

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.

When the brief names collection element identifiers, take them from the source’s own output names and check them against the source test’s rows. A per-row column such as sample can repeat, as when one sample has several runs, so key each element on something unique per dataset and say what makes it unique. A positional suffix (_1, _2) is a mate only when every row it numbers is paired.

Incoming References (27)

nextflow-summary-to-galaxy-reference-data related mold — Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
nextflow-summary-to-galaxy-template related note — gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
Cleanup, sync, and publish non-empty results related mold — Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results.
Fan-in bundle, consume, and flatten related mold — Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
Galaxy: collection patterns related mold — Choose a Galaxy collection operation or map-over recipe from the current and required data shapes.
Galaxy: conditionals patterns related mold — Choose a Galaxy when gate, routed output, fallback, or collection cleanup by what must change downstream.
Galaxy: genomic interval patterns related mold — Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features.
Galaxy: sequence patterns related mold — Use this MOC to choose corpus-grounded Galaxy operations on sequence records (FASTA) — interconvert, reformat, merge, length, extract/mask by region.
Galaxy: tabular patterns related mold — Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
Manifest to mapped collection lifecycle related mold — Use a manifest or table to build a collection, map a tool per row, then relabel or reshape outputs.
Reshape, relabel, and remap by collection axis related mold — Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis.
NEXTFLOW → GALAXY phase of pipeline — Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
Galaxy data-flow draft contract related mold — Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
Galaxy sample_sheet collection types related mold — Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist.
Nextflow conditional to Galaxy subworkflow / when related mold — Stub. Translate Nextflow conditionals into Galaxy `when:` (single workflow). Subworkflow vs inline is an aesthetic call, not a rule.
Nextflow operators to Galaxy collection recipes related mold — Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
Nextflow params to Galaxy workflow inputs related note — Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs.
Nextflow params to Galaxy workflow inputs related mold — Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs.
Nextflow path/glob to Galaxy datatype mapping related note — Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions.
Nextflow path/glob to Galaxy datatype mapping related mold — Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions.
Nextflow reference-data classification related note — Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact.
Nextflow reference-data classification related mold — Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact.
Nextflow-to-Galaxy channel shape mapping related mold — Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes.
Nextflow to Galaxy reference-data mapping related 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 semantics related mold — Defines Nextflow workflow inputs and outputs from docs plus observed fixture pipeline structures.
nf-schema sample sheet validation gaps in Galaxy related mold — nf-schema validation mapped to Galaxy column_definitions: what survives, degrades, or is lost; Galaxy work items + cast loss-recording vocabulary.
Nextflow pipeline summary related note — JSON Schema for the structured summary emitted by the summarize-nextflow Mold.