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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.

Patterngalaxy-tabular-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.
Researchgalaxy-sample-sheet-collections

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).
Researchnextflow-reference-data-classification

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.
Researchnextflow-to-galaxy-reference-data-mapping

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.
Researchnextflow-conditional-to-galaxy-subworkflow-when

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

How to install →

Artifact handoffs

/ pipeline contract

Produces

Consumes

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)