Structured contract copied for validation or lookup.
- Purpose
- Read process, channel, operator, and fixture structure while drafting Galaxy-facing abstract data flow.
nextflow-summary-to-galaxy-data-flow
Translate a Nextflow summary into a Galaxy data-flow 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
11 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 Mold references describe what casting consumes and when the generated skill should load each artifact.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Translate Nextflow channel, tuple, and path shapes into Galaxy dataset and collection shapes.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Classify Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
Workflow-construction idiom. Usually condensed during casting.
- 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.
Workflow-construction idiom. Usually condensed during casting.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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).
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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.
Background synthesis loaded by explicit progressive-disclosure metadata.
- 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 skillnextflow-summary-to-galaxy-data-flow— Translate a Nextflow summary into a Galaxy data-flow design brief.
Artifact handoffs
/ pipeline contractProduces
-
Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
Consumes
-
Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the JSON the data-flow translation reads.
-
Reference-data shape brief from [[nextflow-summary-to-galaxy-reference-data]] that pins per-asset reference inputs and rebuild-on-absence behavior.
-
Preceding Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.
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, unresolved Galaxy tool needs, confidence, and open questions.
The output is not gxformat2 and should not resolve exact Tool Shed tools. nextflow-summary-to-galaxy-template turns this handoff and the interface brief into a skeleton.
Incoming References (25)
- 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.
- Cleanup, sync, and publish non-empty resultsrelated mold— Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results.
- Fan-in bundle, consume, and flattenrelated mold— Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
- Galaxy: collection patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy collection transformation patterns.
- Galaxy: conditionals patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns.
- Galaxy: tabular patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
- Manifest to mapped collection lifecyclerelated 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 axisrelated mold— Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis.
- NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
- Galaxy data-flow draft contractrelated mold— Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
- Galaxy sample_sheet collection typesrelated mold— Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist.
- Nextflow conditional to Galaxy subworkflow / whenrelated mold— Stub. Translate Nextflow conditionals into Galaxy `when:` (single-workflow v1). Subworkflow vs inline is an aesthetic call, not a rule.
- Nextflow operators to Galaxy collection recipesrelated mold— Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
- 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.