Manifest to mapped collection lifecycle

Use this recipe when a source manifest, samplesheet, or tabular list describes repeated work and Galaxy should run one domain tool invocation per row or key.

The reusable value is the handoff from tabular structure into collection map-over, then from mapped outputs back into stable labels or downstream collection shapes.

Recipe

1. Normalize the manifest to the columns that define one unit of work.
2. Build a Galaxy collection from those rows or from Apply Rules-derived identifiers.
3. Connect the collection to the domain tool input so Galaxy maps the tool over elements.
4. Relabel mapped outputs when the tool emits generic or source-derived names, or harmonize sibling collections when paired map-over depends on shared identifiers/order.
5. Reshape, flatten, or unbox paired, nested, or singleton outputs before publication or downstream map-over.

Reach For This When

• A Nextflow samplesheet or tuple(meta, path) stream is being translated into repeated Galaxy collection elements.
• A paper protocol says “run this step for each accession/sample/amplicon/region” and the repeated unit is represented in a table.
• The output collection needs stable sample labels rather than tool-generated names.

Operation Handoffs

• Use tabular-to-collection-by-row when one manifest row becomes one collection element.
• Use collection-build-list-paired-with-apply-rules when manifest columns encode paired inputs.
• Use regex-relabel-via-tabular when mapped outputs need deterministic label cleanup.
• Use harmonize-by-sortlist-from-identifiers when sibling collections from the manifest must align before paired map-over.
• Use collection-flatten-after-fanout when later nested outputs need pooled downstream processing.
• Use collection-swap-nesting-with-apply-rules or collection-unbox-singleton when the mapped output shape is not the shape the next step expects.

Pitfalls

• Do not preserve manifest columns blindly. Keep the columns that define collection identity, pairing, or downstream parameters.
• Do not let tool defaults choose output element identifiers when tests or sibling sync will need stable names.
• Do not use this recipe for simple file-content concatenation or report reduction; use the relevant aggregation operation after map-over.

See Also

• iwc-map-over-lifecycle-survey — Shape A and Nextflow samplesheet mapping evidence.
• galaxy-collection-patterns — collection operation map.