Galaxy: collection patterns

This is the runtime-facing map for Galaxy collection transformation choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation and recipe pages are the actionable references.

Cleanup

• collection-cleanup-after-mapover-failure — use __FILTER_EMPTY_DATASETS__ or __FILTER_FAILED_DATASETS__ after map-over when empty or errored elements would break downstream steps.
• collection-unbox-singleton — use __EXTRACT_DATASET__ with which: first when a known one-element collection must become a dataset.

Map-over Lifecycle Recipes

• manifest-to-mapped-collection-lifecycle — build collection elements from manifest/table rows, map a tool over them, then relabel or reshape outputs.
• cleanup-sync-and-publish-nonempty-results — clean sparse mapped outputs, sync siblings from surviving identifiers, then gate final reports.
• reshape-relabel-remap-by-collection-axis — correct the mapped axis after domain fan-out using Apply Rules and deterministic relabeling.
• fan-in-bundle-consume-and-flatten — bundle parallel outputs for a collection consumer, then flatten or aggregate results.

Identifiers

• sync-collections-by-identifier — membership sync: extract identifiers from one collection and filter or relabel a sibling collection.
• harmonize-by-sortlist-from-identifiers — order sync: sort one sibling collection by another collection’s identifier order.
• regex-relabel-via-tabular — label rewrite: derive new element identifiers in tabular form and apply them with __RELABEL_FROM_FILE__.
• relabel-via-rules-and-find-replace — relabel inside a structural reshape, currently grounded in the influenza fan-out pattern.

Structural Reshape

• collection-flatten-after-fanout — collapse nested collection output to a flat list when the outer axis no longer matters.
• collection-build-named-bundle — assemble individual outputs into a named collection bundle for publishing or downstream fan-in.
• collection-swap-nesting-with-apply-rules — use Apply Rules to swap list:list axes.
• collection-split-identifier-via-rules — use Apply Rules regex columns to derive nested list identifiers from one identifier string.
• collection-build-list-paired-with-apply-rules — use Apply Rules to promote identifier columns into list:paired structure.

Bridges

• tabular-to-collection-by-row — split a tabular manifest/list into collection elements for map-over.
• tabular-concatenate-collection-to-table — row-bind a collection of tabular outputs into one table.
• tabular-pivot-collection-to-wide — outer-join a collection of id/value tabulars into one wide table.

See also

• iwc-transformations-survey — collection-transform survey and evidence trail.
• galaxy-tabular-patterns — companion MOC for tabular operations.