Nextflow: source pattern map

This is the source-facing map for Nextflow-to-Galaxy conversion patterns. Use it when the source evidence is a Nextflow channel shape or operator idiom rather than a Galaxy operation.

The Galaxy pattern library remains the implementation layer. Source-pattern pages should explain what the converter saw in Nextflow, then link to the Galaxy patterns that implement or approximate that source idiom.

Intended operation or recipe pages

• samplesheet-rows-to-galaxy-collections — route fromSamplesheet, splitCsv, and repeated tuple(meta, path) inputs toward Galaxy list, paired, and list:paired collection construction.
• keyed-join-to-identifier-synchronized-mapover — route join and combine(by:) toward identifier extraction, filtering, sorting, and relabeling patterns.
• grouped-channel-to-regrouped-collection — route groupTuple, transpose, and grouped tuple payloads toward nested collections, Apply Rules reshaping, flattening, or domain reduction.
• branch-filter-ifempty-to-galaxy-filters-gates — route branch, .filter, and .ifEmpty toward Galaxy filters, conditional gates, or review triggers.
• mix-collect-to-report-aggregation — route mix, collect, toList, and collectFile toward report aggregation, tabular collapse/pivot, and output bundles.
• mapped-output-cleanup-and-publishing — route mapped output cleanup and publishDir intent toward filtering, relabeling, gating, bundles, and report outputs.

Metadata contract

Each source-pattern page should list the Galaxy implementation pages in implemented_by_patterns. That field is machine-validated to resolve only to type: pattern notes.

Use review_triggers when the Nextflow idiom has semantics Galaxy cannot preserve automatically: unmatched join keys, duplicate keys, remainder, arbitrary tuple records, per-element dynamic branching, or filesystem-specific publishDir layout.

See also

• iwc-map-over-lifecycle-survey — IWC map-over lifecycle survey that motivated this source-pattern layer.
• nextflow-to-galaxy-channel-shape-mapping — prior source-to-target shape mapping.
• nextflow-operators-to-galaxy-collection-recipes — prior operator classification.