Nextflow: mix and collect to report aggregation

Use this when Nextflow report, version, or QC channels converge before final reporting or publication.

Source idioms

• mix(...) merges report, version, or QC channels.
• collect() and toList() reduce many emitted values into one downstream invocation.
• collectFile(...) materializes one file from channel values.

Galaxy translation

• If source emits nested outputs for a report consumer, flatten first with collection-flatten-after-fanout.
• If final artifacts should remain separate but published together, use collection-build-named-bundle.
• If per-element tabular outputs should become one long table, use tabular-concatenate-collection-to-table.
• If per-element id/value tables should become one wide matrix, use tabular-pivot-collection-to-wide.
• If several parallel outputs feed a collection-aware consumer before flattening, use fan-in-bundle-consume-and-flatten.
• If aggregation/reporting should only run when cleaned results remain, use conditional-gate-on-nonempty-result.

Operator-specific decisions

mix

Usually this is Galaxy wiring or bundle construction. Review if order, duplicate identifiers, or mixed file types matter.

collect and toList

Usually this becomes one downstream Galaxy tool invocation over a collection. Pick row-bind, wide-pivot, bundle, or flatten based on the downstream consumer shape.

collectFile

Treat this as one materialized file. Prefer an explicit Galaxy tool or report output. Do not model it as collection assembly unless the downstream object remains a collection.

Evidence posture

This page is grounded in existing Foundry source-shape and lifecycle notes. Direct Nextflow fixture evidence was not regenerated during authoring.