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nextflow-summary-to-galaxy-template

gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.

reviewed source/nextflowtarget/galaxy
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Mold health

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  • 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

    17 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-template
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.

RuntimeUpfrontVerbatimHypothesis
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.
Schema galaxy-workflow-draft

Structured contract copied for validation or lookup.

RuntimeUpfrontVerbatimCast Validated
Purpose
Output contract: the emitted gxformat2 draft conforms to [[galaxy-workflow-draft]]. Cast bundles the JSON Schema so the skill carries its output shape alongside the [[draft-validate]] CLI checks.
CLI Command draft-validate

Command reference. Usually cast to a sidecar and loaded only when invoked.

RuntimeOn DemandSidecarHypothesis
Purpose
Validate the emitted draft against draft-contract rules (sentinel form, topology, _plan_* placement) before handing off.
Trigger
After writing or modifying the draft workflow file.
Verify
Cast the skill, run on a representative Nextflow pipeline, confirm draft-validate diagnostics route back.
Research galaxy-workflow-draft-format

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
Purpose
Emit the gxformat2 draft superset: TODO tool_id, optional tool_state / tool_shed_repository, and per-step _plan_state / _plan_context planning fields.
Verify
Promote after a downstream per-step implementation Mold consumes _plan_state and _plan_context without round-tripping back through the source summary.
Research galaxy-workflow-testability-design

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Choose stable workflow input/output labels, testable checkpoint outputs, and fixture-compatible workflow interfaces while drafting the skeleton.
Trigger
When the template decides workflow inputs, workflow outputs, promoted checkpoints, or collection output identifiers that future tests will need to address.
Research galaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeUpfrontVerbatimHypothesis
Purpose
Respect the handoff from abstract data-flow draft to gxformat2 skeleton.
Trigger
When translating abstract nodes, unresolved tool needs, and placeholder transformations into template TODOs.
Verify
Promote after two worked Nextflow-to-Galaxy templates preserve the data-flow/template split without schema changes.
Pattern galaxy-collection-patterns

Workflow-construction idiom. Copied verbatim; may carry companions.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Use corpus-grounded collection pattern guidance for unresolved skeleton steps.
Trigger
When adding TODO steps for collection cleanup, reshaping, relabeling, identifier synchronization, or collection-tabular bridges.
Pattern galaxy-tabular-patterns

Workflow-construction idiom. Copied verbatim; may carry companions.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Use corpus-grounded tabular pattern guidance for unresolved skeleton steps.
Trigger
When adding TODO steps for tabular filtering, projection, joins, aggregation, text-processing recipes, or tabular-collection bridges.
Pattern galaxy-conditionals-patterns

Workflow-construction idiom. Copied verbatim; may carry companions.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Use corpus-grounded conditional pattern guidance for unresolved skeleton steps.
Trigger
When adding TODO steps for 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; may carry companions.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Use corpus-grounded genomic-interval pattern guidance for unresolved skeleton steps.
Trigger
When adding TODO steps for interval overlap, merge, coverage, windowing, masking, or set-algebra on coordinate features.
Research nextflow-conditional-to-galaxy-subworkflow-when

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Emit `when:` clauses on the right step type (subworkflow vs tool) and the right output fan-in primitive (`pick_value`, modes `first_non_null` / `first_or_skip` / `the_only_non_null`) when the data-flow brief carries a conditional disposition through to the skeleton.
Trigger
When the upstream data-flow brief assigns a source conditional to a subworkflow `when:` or inline `when:` shape, or when emitting the merge step for two or more `when:`-gated branches that produce the same logical output.
Research nextflow-reference-data-classification

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Cross-check source-side reference-data classifications before committing reference assets, optional inputs, and rebuild behavior into the gxformat2 skeleton.
Trigger
When emitting workflow inputs or input-connection wiring for reference assets and 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.
Research nextflow-to-galaxy-reference-data-mapping

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Resolve reference-asset declarations into gxformat2 inputs with the right datatype, optionality, and rebuild-on-absence wiring; cross-check the upstream brief against the datatypes table and v1 posture when the brief is silent or low-confidence on a specific asset.
Trigger
When emitting workflow inputs or input-connection wiring for any reference asset flagged in the reference-data brief (FASTA, fai, dict, indexes, dbsnp, known_indels, intervals, PoN, …), or when the source pipeline declares iGenomes-derived params, per-asset reference path params, or any compute-if-missing index-building branch.
Research galaxy-workflow-comments

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Group the settled step set into titled stage frames (the gxformat2 `comments:` array) so the skeleton carries the analysis-stage narrative IWC authors annotate by hand. Schema-legal and optional.
Trigger
After topology is settled and the skeleton can be partitioned into named analysis stages (inputs, per-stage step clusters, parameter-derivation knots, visualization/outputs).

Cast artifacts

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

nextflow-summary-to-galaxy-template

Read the original Nextflow source artifact, the summary-nextflow.json summary, the Nextflow-to-Galaxy reference-data brief, the Nextflow-to-Galaxy interface brief, and the Nextflow-to-Galaxy data-flow brief. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation Molds.

The reference-data, interface, and data-flow briefs guide the skeleton, but they do not replace source evidence. Treat the prior-step index as the working context: Nextflow source, source summary, reference-data brief, interface brief, data-flow brief, and any open questions carried forward.

Topology is this Mold’s job to settle. The output must be concrete gxformat2: workflow inputs with their final collection shapes and formats, workflow outputs, the step set, the producer→consumer edge graph, branches, and when: guards are all decided here. The upstream interface and data-flow briefs guide those decisions, but if they hedge or leave a topology choice open, this Mold makes the call from source evidence, IWC exemplars, and pattern pages — never emit a topology TODO. Wrapper resolution, by contrast, is evidence-gated, not source-gated: resolve each tool step to the tier its evidence supports — Resolved (fully concrete, no _plan_*), Identity-pinned (concrete tool_id, parameters and changeset left to the per-step Mold), or Deferred (tool_id: TODO) — as defined in galaxy-workflow-draft-format. Capture whatever you defer in the _plan_* family (_plan_state, _plan_context, _plan_in, _plan_out) so the per-step Mold has the source evidence and constraints it needs.

Source tendency: nf-core modules name their tool, pin a version, and carry the command: block, conda packages, and container tags — so steps reach Resolved when a pattern page or IWC exemplar covers the operation (fill tool_id, parameters, and port names from the worked example), and Identity-pinned when the module names the tool but its settings for this context stay open. Deferred is for domain-specific scientific tools with no covering pattern (alignment, variant calling, expression quantification, etc.) — pack _plan_context with the source command, conda specs, container tags, and pre/post conditions the per-step Mold needs to pick a wrapper. Emitting TODO over a pattern-covered recipe discards real evidence the per-step Mold cannot recover.

Optionally, once topology is settled, group the step set into titled stage frames via the gxformat2 comments: array (one frame per analysis stage, contains_steps: populated, color decorative) — see galaxy-workflow-comments for the convention.

Before handing off, check each settled step is computable from what feeds it. The connection graph knows that ports connect, not what they carry — so a declared output that needs evidence no wired input supplies will validate yet can’t be implemented. Where you find that gap, wire (or add) the producer; if you can’t, append a blocking entry to the open-requirements-ledger naming the step, the uncomputable output, and the missing evidence (and record vague intent in _plan_state) so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late. More generally, carry the ledger: read the entries bearing on your topology decisions and mark resolved the ones you close.

Output shape is gxformat2 with wrapper-tier relaxations and _plan_state / _plan_context / _plan_in / _plan_out per tool step — see galaxy-workflow-draft-format. Refinement open work for those planning fields lives in refinement.md.

Incoming References (21)