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Nextflow: samplesheet rows to Galaxy collections

Route Nextflow samplesheet row streams and repeated tuple inputs to Galaxy list, paired, or list:paired collections.

draft source-patternsource/nextflowtarget/galaxy
Revised
2026-05-04
Rev
1
Implemented By
Review Triggers
  • Samplesheet row identity is not unique or stable.
  • Rows encode both single-end and paired-end reads.
  • Paired roles need regex normalization before Galaxy construction.
  • Metadata fields drive downstream parameters, grouping, or branching.
  • Rows encode multiple files that are not paired reads.
  • fromSamplesheet or splitCsv logic mutates the row shape.
Related

Nextflow: samplesheet rows to Galaxy collections

Use this when the source evidence is a samplesheet or manifest reader that emits repeated channel records such as tuple(meta, path(reads)).

Source idiom

  • val(meta) carries identity and attributes; it is not itself a Galaxy dataset.
  • Repeated tuple(meta, path(file)) usually maps to a Galaxy list collection.
  • Repeated tuple(meta, [R1, R2]) usually maps to list:paired.
  • One standalone pair may be paired, but repeated samples should stay list:paired.

Galaxy target choice

Source row payloadGalaxy shapeImplementation route
One file per rowlisttabular-to-collection-by-row or direct collection input
Forward/reverse reads per rowlist:pairedcollection-build-list-paired-with-apply-rules
One pair totalpairedDirect paired input or paired collection construction
Mixed single/paired rowssplit collections or reviewsource review trigger
Extra non-read filesparallel collections or reviewsource review trigger

Implementation route

  1. Preserve stable sample identity from the row metadata.
  2. Decide collection type from file payload shape, not from metadata object shape alone.
  3. If the source starts as a tabular manifest, use tabular-to-collection-by-row.
  4. If pairedness is encoded in columns or identifiers, use collection-build-list-paired-with-apply-rules.
  5. If the workflow maps domain tools per row, use manifest-to-mapped-collection-lifecycle.
  6. After mapped steps, relabel, reshape, or sync only as needed through galaxy-collection-patterns.

Evidence posture

This page is grounded in existing Foundry research notes, especially nextflow-to-galaxy-channel-shape-mapping and iwc-map-over-lifecycle-survey. Generated Nextflow fixtures were not present during authoring, so do not treat this page as direct fixture evidence.

Incoming References (1)

  • Nextflow: source pattern maprelated note— Use this source-pattern map to route recurring Nextflow channel and operator idioms to Galaxy implementation patterns.