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nextflow-summary-to-galaxy-template

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

draft moldsource/nextflowtarget/galaxy
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Mold health

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  • 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

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

Schemagalaxy-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 Commanddraft-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.
Researchgalaxy-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.
Researchgalaxy-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.
Researchgalaxy-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.
Patterngalaxy-tabular-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Patterngalaxy-conditionals-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Patterngalaxy-interval-patterns

Workflow-construction idiom. Usually condensed during casting.

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.
Researchnextflow-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.
Researchnextflow-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.
Researchnextflow-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.

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.

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 (20)