nf-bids

BIDS neuroimaging dataset structure and the bundled libBIDS.sh parser: entities, long/short names, TSV table contract, bidsignore behavior, JSON sidecars. Use when working on parsing, entity handling, or writing BIDS test data or configs.

nf-bids closure-based channel operators groupTupleBy, joinBy, combineBy: signatures, return formats, KeyExtractor/CompositeKey internals, design rationale. Use when using, modifying, or extending these operators.

Debugging playbook for nf-bids: known gotcha catalogue, root-cause methodology for grouping and matching bugs, logging, multi-candidate matching diagnosis. Use when channel output is wrong, groups are missing, files match the wrong config, or changes seem to have no effect.

Nextflow plugin development mechanics for nf-bids. Use when adding operators or factory methods, registering extension points, debugging plugin loading, or when code changes seem to have no effect at runtime.

nf-bids plugin architecture: runtime flow of Channel.fromBIDS, set handler routing, suffix mapping design, flat output shaping, cross-modal broadcasting. Use when navigating the codebase, tracing data flow, or modifying handlers/output structure.