map 15 links
Galaxy: collection patterns
Use this MOC to choose corpus-grounded Galaxy collection transformation patterns.
IWC-grounded workflow construction recipes.
Pattern maps are the entry points; operation and recipe pages are the concrete Galaxy authoring moves that Molds can reference and casts can condense.
- Total
- 44
- Maps
- 3
Pattern Maps
/ start here map 5 links
Galaxy: conditionals patterns
Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns.
map 14 links
Galaxy: tabular patterns
Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
Browse By Topic
/ tag rollupsCollection
/ 11 implementation patterns draft operation
Collection: build list paired with Apply Rules
Use Apply Rules to promote identifier columns into a list:paired collection, with optional cleanup first.
draft operation
Collection: build named bundle
Use BUILD_LIST to assemble named outputs into a collection bundle for publishing or downstream fan-in.
draft operation
Collection: cleanup after map-over failure
Use FILTER_EMPTY or FILTER_FAILED after map-over when bad elements would break downstream collection steps.
draft operation
Collection: flatten after fan-out
Use FLATTEN to collapse nested collection outputs to a flat list once the outer axis no longer matters.
draft operation
Collection: harmonize by sortlist from identifiers
Use SORTLIST with sort_type:file to reorder one collection by another collection's identifiers.
draft operation
Collection: regex relabel via tabular
Derive collection element identifiers in a tabular mapping, then apply them with RELABEL_FROM_FILE.
draft recipe
Collection: relabel via rules and find/replace
Use Apply Rules, identifier extraction, find/replace, and relabeling for structural fan-out cleanup.
draft operation
Collection: split identifier via rules
Use Apply Rules regex columns to split one collection identifier into nested list identifiers.
draft operation
Collection: swap nesting with Apply Rules
Use Apply Rules to regroup a list:list collection by swapping outer and inner identifier columns.
draft operation
Collection: sync collections by identifier
Use collection_element_identifiers with FILTER_FROM_FILE or RELABEL_FROM_FILE to align sibling collections.
draft operation
Collection: unbox singleton
Use __EXTRACT_DATASET__ with which: first when a one-element collection must become a dataset.
Conditional
/ 4 implementation patterns draft recipe
Conditional: gate on non-empty result
Derive a boolean from empty or non-empty data, then use when to skip reporting or export steps.
draft operation
Conditional: route between alternative outputs
Use when-gated alternatives plus pick_value to merge binary or one-of-N routes into one downstream value.
draft operation
Conditional: run optional step
Use a workflow boolean connected as inputs.when to skip an optional Galaxy step or branch.
draft operation
Conditional: transform or pass through
Gate an optional transform, then use pick_value to pass transformed data when present or original data otherwise.
General
/ 8 implementation patterns draft recipe
Cleanup, sync, and publish non-empty results
Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results.
draft recipe
Fan-in bundle, consume, and flatten
Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
draft recipe
Manifest to mapped collection lifecycle
Use a manifest or table to build a collection, map a tool per row, then relabel or reshape outputs.
draft operation
nf-core channel input → Galaxy data / collection
Map an nf-core process's tuple(meta, path) input channel to a Galaxy <param type="data"> or paired/list collection input.
draft operation
nf-core meta-map → Galaxy params
Promote nf-core meta-map keys to Galaxy <param>s only when they drive script behavior; drop identity-only keys; pull naming from $input.element_identifier.
draft operation
nf-core task.ext.args → Galaxy additional-options bag
Map nf-core's task.ext.args escape hatch to a single Galaxy text param surfacing extra command-line arguments.
draft operation
nf-core versions emit → Galaxy <version_command>
Translate nf-core's versions emit (heredoc or topic: versions) into Galaxy's <version_command>, dropping the versions output channel.
draft recipe
Reshape, relabel, and remap by collection axis
Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis.
nf-core stub
/ 1 implementation pattern draft operation
nf-core stub: block → Galaxy (intentional drop)
nf-core's stub: block has no Galaxy analog; the convert Mold drops it intentionally and records the drop in _provenance.yml.
Parameter
/ 3 implementation patterns draft operation
Parameter: compose runtime text parameter
Use compose_text_param to build connected text expressions from constants plus runtime scalar values.
draft operation
Parameter: derive from file
Read a one-value dataset with param_value_from_file, including count recipes that feed typed parameters.
draft operation
Parameter: map workflow enum to tool parameter
Use map_param_value to translate workflow enum values into downstream tool codes, flags, or snippets.
Tabular
/ 14 implementation patterns draft operation
Tabular: compute a new column
Use column_maker (Add_a_column1) with strict error_handling to insert/replace a computed column. Per-expression-kind auto_col_types rule.
draft operation
Tabular: concatenate collection to table
Use collapse_dataset to row-bind a collection of tabulars into one table, with optional element IDs and header dedupe.
draft operation
Tabular: cut and reorder columns
Use Cut1 with a comma-separated cN list to project — and reorder — columns. Listing out of order is the canonical reorder idiom.
draft operation
Tabular: filter rows by column value
Use Filter1 with a Python expression over cN columns to drop rows. Highest-frequency tabular row filter in IWC.
draft operation
Tabular: filter rows by regex
Use tp_grep_tool for whole-line regex row filters on tabular input. Grep1 is the legacy alternative.
draft operation
Tabular: group and aggregate
Use datamash_ops for grouped tabular aggregation: multi-column grouping, collapse, countunique, min/max, and reductions.
draft operation
Tabular: join on key
Use tp_easyjoin_tool for two-tabular key joins; use tp_multijoin_tool for many files and query_tabular for SQL joins.
draft operation
Tabular: pivot collection to wide
Use collection_column_join to outer-join a collection of 2-column id/value tables into one wide table.
draft operation
Tabular: prepend header
Use tp_awk_tool to prepend a constant header line, optionally skipping or reformatting an existing first row.
draft operation
Tabular: relabel by row counter
Use tp_awk_tool to replace each row or label with deterministic sample_N values from awk NR.
draft operation
Tabular: split taxonomy string
Use tp_awk_tool to split semicolon-delimited taxonomy strings into explicit rank columns with missing-rank handling.
draft operation
Tabular: SQL query
Use query_tabular when SQL semantics justify it: windows, joins, anti-joins, or fused project+compute over tabulars.
draft operation
Tabular: synthesize BED from 3-column input
Use tp_awk_tool to convert chrom/start/end rows into 6-column BED, subtracting 1 from start and setting constants.
draft operation
Tabular: to collection by row
Use split_file_to_collection split_by:col to fan a tabular into collection elements by row/key.