Every note in the Foundry.

cli/ (23)

• Cwl Utils cli-tool CWL document utilities. summarize-cwl uses cwl-normalizer to gather references and upgrade to v1.2 JSON.
• Cwltool cli-tool Reference CWL runner and validator. Used by summarize-cwl for entrypoint validation.
• Foundry cli-tool Foundry CLI: bundles all Mold IO validators and a summarize-nextflow subcommand.
• foundry summarize-nextflow cli-command Statically introspect a Nextflow / nf-core pipeline tree and emit a validated JSON summary.
• foundry validate-galaxy-tool-discovery cli-command AJV gate for discover-shed-tool recommendation documents.
• foundry validate-galaxy-tool-summary cli-command AJV gate for galaxy-tool-cache summarize manifests, including the nested parsed_tool subtree.
• foundry validate-summary-cwl cli-command AJV gate for summarize-cwl JSON documents.
• foundry validate-summary-nextflow cli-command AJV gate for summarize-nextflow JSON documents.
• foundry validate-tests-format cli-command AJV gate for Galaxy workflow tests YAML, with optional workflow cross-check.
• Gxwf cli-tool Galaxy workflow design-time CLI (validate, convert, lint, roundtrip, tool-cache discovery).
• gxwf convert cli-command Convert a Galaxy workflow between native (.ga) and format2 (.gxwf.yml) representations.
• gxwf tool-revisions cli-command Resolve a Tool Shed tool to changeset revisions for reproducible workflow pinning. Final step in discover-and-pin.
• gxwf tool-search cli-command Free-text Tool Shed search returning candidate tools as JSON; first step in the discover-and-pin sequence.
• gxwf tool-versions cli-command List TRS-published versions of a Tool Shed tool, oldest→newest. Second step in the discover-and-pin sequence.
• gxwf validate cli-command Validate Galaxy workflow structure, tool state, and optional connection compatibility before runtime execution.
• gxwf validate-tests cli-command Validate Galaxy workflow test files and optionally cross-check labels against their workflow.
• Planemo cli-tool Galaxy tool/workflow runtime testing CLI; used by run-workflow-test and friends.
• planemo cli_metadata cli-command Export structured metadata for Planemo CLI commands.
• planemo lint cli-command Check for common errors and best practices.
• planemo output_schema cli-command Export JSON Schemas for Planemo machine-readable outputs.
• planemo test cli-command Run specified tool or workflow tests within Galaxy.
• planemo workflow_test_init cli-command Initialize a Galaxy workflow test description for supplied workflow.
• planemo workflow_test_on_invocation cli-command Run defined tests against existing workflow invocation.

molds/ (37)

• author-galaxy-tool-wrapper mold Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.
• compare-against-iwc-exemplar mold Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.
• convert-nfcore-module-to-galaxy-tool mold Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
• cwl-summary-to-galaxy-data-flow mold Translate a CWL summary into a Galaxy data-flow design brief.
• cwl-summary-to-galaxy-interface mold Map a CWL summary into a Galaxy workflow interface design brief.
• cwl-summary-to-galaxy-template mold gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
• cwl-test-to-galaxy-test-plan mold Translate CWL test fixtures into a Galaxy workflow test plan.
• debug-cwl-workflow-output mold Triage failing CWL run outputs; classify failure modes; propose fixes.
• debug-galaxy-workflow-output mold Triage failing Galaxy run outputs; classify failure modes; propose fixes.
• discover-shed-tool mold Search the Tool Shed for an existing wrapper, drill from hit to a pinnable changeset, classify candidates, and recommend or fall through.
• find-test-data mold Search IWC fixtures and public sources for test data matching a data-flow shape.
• implement-cwl-tool-step mold Convert an abstract step into a concrete CWL CommandLineTool + step.
• implement-cwl-workflow-test mold Assemble CWL job file(s) and expected-output assertions.
• implement-galaxy-tool-step mold Convert an abstract step into a concrete gxformat2 step using a tool summary.
• implement-galaxy-workflow-test mold Assemble Galaxy workflow test fixtures and assertions.
• nextflow-summary-to-cwl-data-flow mold Translate a Nextflow summary into a CWL data-flow design brief.
• nextflow-summary-to-cwl-interface mold Map a Nextflow summary into a CWL Workflow interface design brief.
• nextflow-summary-to-galaxy-data-flow mold Translate a Nextflow summary into a Galaxy data-flow design brief.
• nextflow-summary-to-galaxy-interface mold Map a Nextflow summary into a Galaxy workflow interface design brief.
• nextflow-summary-to-galaxy-reference-data mold Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
• nextflow-summary-to-galaxy-template mold gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
• nextflow-test-to-cwl-test-plan mold Translate Nextflow test evidence into a CWL workflow test plan.
• nextflow-test-to-galaxy-test-plan mold Translate Nextflow test evidence into a Galaxy workflow test plan.
• paper-summary-to-cwl-design mold Translate a paper summary into a CWL workflow design brief.
• paper-summary-to-galaxy-design mold Translate a paper summary into a Galaxy workflow design brief.
• paper-summary-to-galaxy-template mold gxformat2 skeleton with per-step TODOs from a paper summary and the paper-to-Galaxy design brief.
• paper-to-test-data mold Derive workflow test inputs and expected outputs from a paper.
• run-workflow-test mold Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
• summarize-cwl mold Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.
• summarize-cwl-tool mold Derive a CommandLineTool description (container, baseCommand, IO) for a CWL target.
• summarize-galaxy-tool mold Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.
• summarize-nextflow mold Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds.
• summarize-paper mold Extract methods, tools, sample data, and references from a paper.
• summary-to-cwl-template mold CWL Workflow skeleton with per-step TODOs from source and design handoffs.
• validate-cwl mold Run cwltool --validate / schema lint, classify failures, recommend fixes.
• validate-galaxy-step mold Run gxwf validation on the just-implemented Galaxy step and route failures back to step implementation.
• validate-galaxy-workflow mold Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.

patterns/ (44)

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

pipelines/ (5)

• CWL → GALAXY pipeline Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
• NEXTFLOW → CWL pipeline Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.
• NEXTFLOW → GALAXY pipeline Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
• PAPER → CWL pipeline Direct path from a paper to a CWL Workflow + CommandLineTool set.
• PAPER → GALAXY pipeline Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.

research/ (52)

• Component Archon research Archon as a possible Foundry harness substrate; strong fit for heavy harnesses, with per-step sub-DAG looping as the main gap.
• CWL workflow anatomy research CWL structure relevant to summarize-cwl: normalized documents, steps, scatter, conditionals, requirements, and dependency handling.
• Component Nextflow Channel Operators research Structured digest of Nextflow channel operators (47 entries) with cardinality and shape semantics; backs summarize-nextflow §6 edge reconciliation.
• Component Nextflow Containers And Envs research Container URL grammar (depot, BioContainers, mulled-v2, Wave, ORAS) and conda directive resolution rules backing summarize-nextflow §5.
• Component Nextflow Inspect research White paper on Nextflow's native introspection subcommands — `nextflow inspect`, `nextflow config`, and adjacent tooling. Survey, not decision.
• Component Nextflow Pipeline Anatomy research Stub. DSL2 layout, channel idioms, operator-chain reading rules. Grows from cast contact with rnaseq/sarek/ad-hoc — see issue #17.
• Component Nextflow Testing research nf-test patterns mapped to Galaxy planemo asserts and CWL test equivalents — backs nextflow-test-to-target-tests Mold and summarize-nextflow §7.
• Component Nf Core Module Conventions research RFC 2119 conventions enforced by nf-core/tools module lint, with lint-check pointers. Backs summarize-nextflow + author-galaxy-tool-wrapper.
• Component Nf Core Tools research White paper on nf-core/tools — conventions, CLI surface, schema universe, container resolution. Survey, not decision.
• Component Tool Shed Search research Tool Shed's Whoosh repo/tool search and partial GA4GH TRS v2, indexed from hg-walked metadata with no auto-refresh on upload
• CWL pickValue → Galaxy pick_value (post galaxy#22222) research CWL `pickValue` (first_non_null / the_only_non_null / all_non_null) → Galaxy's native `pick_value` workflow step added by galaxyproject/galaxy#22222.
• CWL v1.2 schema documents research Vendored official CWL v1.2.1 JSON/SALAD schema documents used as source-structure reference for CWL summarization.
• CWL when:/pickValue → Galaxy branching translation research CWL `when:`/`pickValue` → Galaxy. Three honest translations (paired_or_unpaired input, native pick_value step, sibling workflows) plus how to pick among them.
• Galaxy Apply Rules DSL research Reference for Galaxy's Apply Rules DSL: rule operations, mapping operations, composition patterns, pitfalls.
• Galaxy collection semantics research Vendored formal spec of Galaxy dataset-collection mapping/reduction semantics, with labeled examples and pinned test references.
• Galaxy collection-operation tools research Catalog of Galaxy's collection-operation tools — purpose, IO, parameters, selection guide. Companion to galaxy-collection-semantics.
• Galaxy data-flow draft contract research Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
• Galaxy datatypes registry sample research Vendored Galaxy datatypes registry sample: extension → datatype class mapping, sniff order, converters, and display applications.
• Galaxy <discover_datasets> research Reference for the <discover_datasets> Galaxy XML element — attributes, named/regex patterns, <data> vs <collection> contexts, test assertions.
• Galaxy native workflow (.ga) structural JSON Schema research Vendored structural JSON Schema for Galaxy native workflow (.ga) format: vocabulary for the JSON shape Galaxy emits and consumes.
• Galaxy paired_or_unpaired collection type research Galaxy's `paired_or_unpaired` collection type: discriminated-union shape for paired-or-single reads, no workflow-level mode switch needed. Galaxy PR #19377.
• Galaxy sample_sheet collection types research Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist.
• Galaxy tool and job failure reference research Reference for Galaxy tool stdio rules, job failure detection, job states, and job API failure surfaces.
• Galaxy tool summary input source research Decides that summarize-galaxy-tool reads cached ParsedTool JSON as its v1 input source.
• Galaxy workflow draft format research gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.
• Galaxy workflow invocation failure reference research Reference for Galaxy workflow invocation states, messages, failure reasons, and invocation API surfaces.
• Galaxy Workflow Testability Design research Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible.
• Galaxy tool XML schema research Vendored Galaxy tool XML schema for wrapper structure, parameters, outputs, tests, and assertion syntax.
• gxformat2 structural JSON Schema research Vendored structural JSON Schema for gxformat2 workflows: vocabulary for inputs, outputs, steps, and step subtypes.
• gxformat2 workflow inputs research Conceptual model, current aliases, and schema gaps for gxformat2 workflow inputs.
• Alignment: gxy-sketches ↔ Galaxy Workflow Foundry research Where the Foundry's per-source summary Molds align with gxy-sketches on field names and source/test-fixture vocabulary, and where they intentionally do not.
• Iwc Conditionals Survey research Corpus survey of Galaxy conditional step usage in IWC, covering when-gates, boolean shims, and routed output selection.
• Iwc Map Over Lifecycle Survey research Survey of IWC map-over lifecycle recipes, with a Nextflow-to-Galaxy crosswalk for collection construction, cleanup, reshape, reduce, and publish phases.
• Iwc Parameter Derivation Survey research Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters.
• Iwc Runtime Parameter Shims Survey research Focused survey of tiny IWC runtime parameter shims for flags, enums, counts, booleans, and composed text.
• Iwc Shortcuts Anti Patterns research What IWC test suites cut corners on (accepted) vs what's a code smell — existence-only probes, sim_size deltas, image dim checks, label coupling.
• Iwc Tabular Operations Survey research Corpus survey of tabular tools and operations across IWC workflows; map for the operation pattern hierarchy on row/column data manipulation.
• Iwc Test Data Conventions research How IWC workflows organize and reference test data — Zenodo-first, SHA-1 integrity, collection shapes, CVMFS gotchas.
• Iwc Transformations Survey research Corpus survey of collection-shape transformations across IWC: built-in collection ops, toolshed transformers, and the multi-step recipes that bracket map-over.
• Iwc Workflow Testability Survey research IWC evidence survey for Galaxy workflow structures that make workflow tests meaningful.
• Nextflow conditional to Galaxy subworkflow / when research Stub. Translate Nextflow conditionals into Galaxy `when:` (single-workflow v1). Subworkflow vs inline is an aesthetic call, not a rule.
• Nextflow operators to Galaxy collection recipes research Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
• Nextflow params to Galaxy workflow inputs research Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs.
• Nextflow path/glob to Galaxy datatype mapping research Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions.
• Nextflow reference-data classification research Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact.
• Nextflow nf-test snapshots to Galaxy/Planemo assertions research Translates nf-test snapshot assertions into Galaxy workflow test-format assertions, broken out by module-level vs pipeline-level test shape.
• Nextflow-to-Galaxy channel shape mapping research Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes.
• Nextflow to Galaxy reference-data mapping research Galaxy-side translation of Nextflow reference-data classifications: idioms available, the v1 posture, datatype defaults, and the in-tool rebuild trade-off.
• Nextflow workflow I/O semantics research Defines Nextflow workflow inputs and outputs from docs plus observed fixture pipeline structures.
• nf-schema sample sheet validation gaps in Galaxy research nf-schema validation mapped to Galaxy column_definitions: what survives, degrades, or is lost; Galaxy work items + cast loss-recording vocabulary.
• Planemo Asserts Idioms research Decision and idiom guide for picking planemo workflow-test assertions: which family per output type, how to size tolerances, when to validate.
• Planemo workflow-test architecture research Reference for Planemo workflow test/run architecture, Galaxy modes, API polling, and noisy failure boundaries.

schemas/ (10)

• Galaxy tool discovery recommendation schema JSON Schema for Tool Shed discovery hit, weak, and miss recommendations.
• Galaxy tool summary manifest schema JSON Schema for the deterministic per-tool manifest emitted by `galaxy-tool-cache summarize`.
• Nextflow parameter schema (nf-schema meta-schema) schema JSON Schema (Draft 2020-12) meta-schema validating per-pipeline nextflow_schema.json files. Upstream from nextflow-io/nf-schema.
• nf-core module meta.yml schema schema JSON Schema (Draft-07) validating nf-core module meta.yml — channel IO, tools, containers, conda lockfiles. Upstream from nf-core/modules.
• nf-core subworkflow meta.yml schema schema JSON Schema (Draft-07) validating nf-core subworkflow meta.yml — channel IO, components dependencies, authors. Upstream from nf-core/modules.
• Galaxy ParsedTool schema JSON Schema for the upstream Galaxy `ParsedTool` model, vendored from `@galaxy-tool-util/schema`.
• Planemo test report (JSON) schema JSON Schema for the report emitted by `planemo test --test_output_json` (and friends), vendored from upstream planemo.
• CWL workflow summary schema JSON Schema for the structured summary emitted by the summarize-cwl Mold.
• Nextflow pipeline summary schema JSON Schema for the structured summary emitted by the summarize-nextflow Mold.
• Galaxy workflow test format schema JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.

source-patterns/ (7)

• Nextflow: branch, filter, and ifEmpty to Galaxy filters and gates source-pattern Route Nextflow branch, filter, and ifEmpty channel idioms to Galaxy collection cleanup, identifier filters, when gates, or review.
• Nextflow: grouped channel to regrouped Galaxy collection source-pattern Route Nextflow groupTuple, transpose, and grouped tuple payloads to Galaxy collection reshape patterns when the key is a real axis.
• Nextflow: keyed join/combine(by:) to identifier-synchronized map-over source-pattern Route Nextflow keyed joins and combine(by:) pairings to Galaxy collection identifier sync, ordering, relabeling, or table joins.
• Nextflow: mapped output cleanup and publishing source-pattern Route Nextflow mapped-output cleanup and publishDir-style intent to Galaxy filtering, relabeling, gating, bundling, and reports.
• Nextflow: mix and collect to report aggregation source-pattern Route Nextflow mix, collect, toList, and collectFile report fan-in idioms to Galaxy aggregation and bundle patterns.
• Nextflow: source pattern map source-pattern Use this source-pattern map to route recurring Nextflow channel and operator idioms to Galaxy implementation patterns.
• Nextflow: samplesheet rows to Galaxy collections source-pattern Route Nextflow samplesheet row streams and repeated tuple inputs to Galaxy list, paired, or list:paired collections.

docs/ (7)