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Collection: build named bundle

Use BUILD_LIST to assemble named outputs into a collection bundle for publishing or downstream fan-in.

draft target/galaxytopic/galaxy-transformtopic/collection-transform
Revised
2026-09-14
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3
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  • IWC exemplar anchors

    2 abstract workflow anchors declared.

  • Foundry verification fixture

    1 verification path declared.

  • Pattern map coverage

    1 pattern map link here.

  • Metadata contract

    Pattern frontmatter matches the site contract.

Collection: build named bundle

Tool

Use Galaxy built-in __BUILD_LIST__.

The survey found two useful sub-cases:

  • Manual-id output bundle: collect related outputs into a named result collection for organization or publishing.
  • Identifier-id fan-in: assemble tool outputs into one collection for a downstream tool that expects collection input.

__MERGE_COLLECTION__ is the sibling operation when the inputs are already collections. Current corpus evidence does not justify a standalone merge pattern.

When to reach for it

Use __BUILD_LIST__ when you start with individual datasets or individual output connections and need a Galaxy list.

Use manual identifiers when element names should be human-authored result labels. Use inherited identifiers when downstream semantics already know those names.

Do not use this to concatenate file contents. Use tabular-concatenate-collection-to-table when the goal is one combined tabular dataset.

Parameters

datasets is a repeat. Each entry pairs the connected input with an id_cond naming where that element’s identifier comes from:

tool_id: __BUILD_LIST__
tool_state:
  datasets:
    - input: { __class__: ConnectedValue }
      id_cond:
        id_select: manual
        identifier: bray_curtis_pcoa_results

Connect slot N through datasets_N|input.

  • id_select: manual: human-authored names for output bundles. Carries an identifier sub-field.
  • id_select: identifier: inherit the source element identifier, falling back to the dataset name. __EXTRACT_DATASET__ renames its output after the element it pulled, so identifiers survive that hop.
  • id_select: idx: the repeat index, numbered from 0. The default; avoid when element identity matters.

Pitfalls

  • Manual identifiers become collection element identifiers and may appear in output histories or reports.
  • Two entries sharing one identifier collapse to a single element holding the later dataset. Identifiers are dictionary keys — no duplicate, no error.
  • Manual bundles group outputs; they do not align rows, merge contents, or validate common keys.
  • Use inherited identifiers only when source names are meaningful.
  • Prefer __MERGE_COLLECTION__ only when inputs are already collections.

See also

IWC exemplars 2 anchors

IWC Exemplars

amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations high

Groups QIIME2 plots, PCoA results, distance matrices, and richness vectors into named output collections.

microbiome/mags-building/MAGs-generation high

Assembles bin-table outputs from multiple binners into one collection for binette.

Incoming References (8)

  • Collection: flatten after fan-out related pattern — Use FLATTEN to collapse nested collection outputs to a flat list once the outer axis no longer matters.
  • Fan-in bundle, consume, and flatten related pattern — Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
  • Galaxy: collection patterns related pattern — Choose a Galaxy collection operation or map-over recipe from the current and required data shapes.
  • Galaxy Apply Rules DSL related note — Reference for Galaxy's Apply Rules DSL: rule operations, mapping operations, composition patterns, pitfalls.
  • Iwc Map Over Lifecycle Survey related pattern — Survey of IWC map-over lifecycle recipes, with a Nextflow-to-Galaxy crosswalk for collection construction, cleanup, reshape, reduce, and publish phases.
  • Iwc Transformations Survey related note — Corpus survey of collection-shape transformations across IWC: built-in collection ops, toolshed transformers, and the multi-step recipes that bracket map-over.
  • Nextflow: mapped output cleanup and publishing implemented_by_patterns — Route Nextflow mapped-output cleanup and publishDir-style intent to Galaxy filtering, relabeling, gating, bundling, and reports.
  • Nextflow: mix and collect to report aggregation implemented_by_patterns — Route Nextflow mix, collect, toList, and collectFile report fan-in idioms to Galaxy aggregation and bundle patterns.