Galaxy Workflow Foundry.
A sectioned operating view over the knowledge base and casting pipeline for Galaxy workflows.
- Notes
- 242
- Sections
- 8
Pipelines (7)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| INTERVIEW → GALAXY | Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff. | reviewed | 2026-07-24 | 2 |
| NEXTFLOW → GALAXY | Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow. | reviewed | 2026-07-24 | 4 |
| UPDATE-INTERVIEW → GALAXY | Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop. | reviewed | 2026-07-24 | 2 |
| CWL → GALAXY | Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction. | draft | 2026-04-30 | 2 |
| NEXTFLOW → CWL | Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set. | draft | 2026-04-30 | 2 |
| PAPER → CWL | Direct path from a paper to a CWL Workflow + CommandLineTool set. | draft | 2026-04-30 | 2 |
| PAPER → GALAXY | Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate. | draft | 2026-04-30 | 2 |
Molds (47)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| compare-against-iwc-exemplar | Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring. | reviewed | 2026-08-04 | 9 |
| find-test-data | Search IWC fixtures and public sources for test data matching a data-flow shape. | reviewed | 2026-08-04 | 4 |
| repair-galaxy-draft-topology | Re-wire a Galaxy draft region when a step's declared output can't be computed from its wired inputs. | draft | 2026-08-04 | 2 |
| advance-galaxy-draft-step | Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate. | reviewed | 2026-07-24 | 3 |
| apply-galaxy-workflow-changeset | Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps. | reviewed | 2026-07-24 | 2 |
| author-galaxy-tool-wrapper | Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable. | reviewed | 2026-07-24 | 4 |
| changeset-to-galaxy-test-plan | Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan. | reviewed | 2026-07-24 | 2 |
| debug-cwl-workflow-output | Triage failing CWL run outputs; classify failure modes; propose fixes. | draft | 2026-07-24 | 3 |
| debug-galaxy-workflow-output | Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs. | reviewed | 2026-07-24 | 5 |
| discover-shed-tool | Search the Tool Shed for an existing wrapper, drill from hit to a pinnable changeset, classify candidates, and recommend or fall through. | reviewed | 2026-07-24 | 5 |
| freeform-summary-to-galaxy-data-flow | Translate a free-form source summary into a Galaxy data-flow design brief. | reviewed | 2026-07-24 | 2 |
| freeform-summary-to-galaxy-interface | Map a free-form source summary into a Galaxy workflow interface design brief. | reviewed | 2026-07-24 | 2 |
| freeform-summary-to-galaxy-template | gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief. | reviewed | 2026-07-24 | 5 |
| freeform-summary-to-galaxy-test-plan | Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs. | reviewed | 2026-07-24 | 2 |
| implement-cwl-tool-step | Convert an abstract step into a concrete CWL CommandLineTool + step. | draft | 2026-07-24 | 2 |
| implement-cwl-workflow-test | Assemble CWL job file(s) and expected-output assertions. | draft | 2026-07-24 | 2 |
| implement-galaxy-tool-step | Convert an abstract step into a concrete gxformat2 step using a tool summary. | reviewed | 2026-07-24 | 8 |
| implement-galaxy-workflow-test | Assemble Galaxy workflow test fixtures and assertions. | reviewed | 2026-07-24 | 8 |
| interview-to-freeform-summary | Normalize a free-form user interview into the shared freeform-summary workflow handoff. | reviewed | 2026-07-24 | 3 |
| interview-to-galaxy-workflow-changeset | Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set. | reviewed | 2026-07-24 | 2 |
| nextflow-summary-to-galaxy-data-flow | Translate a Nextflow summary into a Galaxy data-flow design brief. | reviewed | 2026-07-24 | 5 |
| nextflow-summary-to-galaxy-interface | Map a Nextflow summary into a Galaxy workflow interface design brief. | reviewed | 2026-07-24 | 5 |
| nextflow-summary-to-galaxy-reference-data | Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline. | reviewed | 2026-07-24 | 4 |
| nextflow-summary-to-galaxy-template | gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs. | reviewed | 2026-07-24 | 8 |
| nextflow-test-to-galaxy-test-plan | Translate Nextflow test evidence into a Galaxy workflow test plan. | reviewed | 2026-07-24 | 5 |
| nextflow-to-test-data | Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs. | reviewed | 2026-07-24 | 2 |
| paper-to-test-data | Derive workflow test inputs and expected outputs from a paper. | draft | 2026-07-24 | 2 |
| run-workflow-test | Execute a workflow's tests via Planemo; emit structured pass/fail and outputs. | reviewed | 2026-07-24 | 6 |
| summarize-cwl-tool | Derive a CommandLineTool description (container, baseCommand, IO) for a CWL target. | draft | 2026-07-24 | 2 |
| summarize-galaxy-tool | Pull JSON schema, container, source, inputs/outputs for a Galaxy tool. | reviewed | 2026-07-24 | 8 |
| summarize-galaxy-workflow | Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps. | reviewed | 2026-07-24 | 2 |
| summarize-nextflow | Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds. | reviewed | 2026-07-24 | 14 |
| summarize-paper | Extract methods, tools, sample data, and references from a paper. | draft | 2026-07-24 | 2 |
| validate-cwl | Run cwltool --validate / schema lint, classify failures, recommend fixes. | draft | 2026-07-24 | 3 |
| validate-galaxy-workflow | Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures. | reviewed | 2026-07-24 | 4 |
| cwl-to-test-data | Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs. | draft | 2026-07-17 | 1 |
| convert-nfcore-module-to-galaxy-tool | Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks). | draft | 2026-06-19 | 4 |
| cwl-summary-to-galaxy-template | gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs. | draft | 2026-06-11 | 4 |
| cwl-summary-to-galaxy-data-flow | Translate a CWL summary into a Galaxy data-flow design brief. | draft | 2026-05-10 | 2 |
| cwl-summary-to-galaxy-interface | Map a CWL summary into a Galaxy workflow interface design brief. | draft | 2026-05-10 | 2 |
| summarize-cwl | Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation. | draft | 2026-05-10 | 2 |
| freeform-summary-to-cwl-design | Translate a free-form source summary into a CWL workflow design brief. | draft | 2026-05-05 | 1 |
| nextflow-summary-to-cwl-data-flow | Translate a Nextflow summary into a CWL data-flow design brief. | draft | 2026-05-05 | 1 |
| nextflow-summary-to-cwl-interface | Map a Nextflow summary into a CWL Workflow interface design brief. | draft | 2026-05-05 | 1 |
| summary-to-cwl-template | CWL Workflow skeleton with per-step TODOs from source and design handoffs. | draft | 2026-05-05 | 2 |
| cwl-test-to-galaxy-test-plan | Translate CWL test fixtures into a Galaxy workflow test plan. | draft | 2026-05-03 | 2 |
| nextflow-test-to-cwl-test-plan | Translate Nextflow test evidence into a CWL workflow test plan. | draft | 2026-05-03 | 1 |
Patterns (54)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| Galaxy: genomic interval patterns | Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features. | draft | 2026-08-03 | 2 |
| Galaxy: sequence patterns | Use this MOC to choose corpus-grounded Galaxy operations on sequence records (FASTA) — interconvert, reformat, merge, length, extract/mask by region. | draft | 2026-08-03 | 2 |
| Interval: consensus regions by multi-intersect | Find features reproducible across replicates: multi-intersect per-replicate sets, threshold by replicate count, then intersect back against the merged call. | draft | 2026-06-10 | 1 |
| Interval: compute coverage | Two coverage modes: genome-wide depth as a bedgraph (genomecoveragebed) and reads counted in given regions (coveragebed). Same family, different question. | draft | 2026-06-10 | 1 |
| Interval: build a mask by set algebra | Compute regions from regions: concatenate candidate intervals, merge into non-overlapping spans, then subtract the set to keep. The gops_* set-algebra recipe. | draft | 2026-06-10 | 1 |
| Interval: merge overlapping features | Collapse overlapping or book-ended intervals within one set into single spans; bedtools mergebed or the gops_merge Operate-on-Genomic-Intervals tool. | draft | 2026-06-10 | 1 |
| Interval: filter or annotate by overlap | Keep, drop, or annotate coordinate features by overlap with a second feature set; bedtools intersect (BED) or vcfvcfintersect (VCF), mapped over a collection. | draft | 2026-06-10 | 1 |
| Interval: window or flank features | Extend features by a fixed or fractional amount to build neighborhood windows, clamped to chromosome ends; bedtools slopbed with a genome file. | draft | 2026-06-10 | 1 |
| Interval: windowed coverage around features | Quantify signal in fixed neighborhoods around point features: window the features (slop), collapse overlaps (merge), then count reads in each window (coverage). | draft | 2026-06-10 | 1 |
| Sequence: relabel FASTA headers via tabular | Edit FASTA headers you cannot easily regex in place: fasta2tab, rewrite column 1 with find/replace, then tab2fasta back. The high-value sequence recipe. | draft | 2026-06-10 | 1 |
| Sequence: compute record lengths | Emit a (id, length) table from a FASTA so downstream tabular steps can filter, sort, or threshold records by length; fasta_compute_length. | draft | 2026-06-10 | 1 |
| Sequence: extract or mask by region | Turn coordinates into sequence: extract FASTA at BED intervals (getfasta), mask regions by BED (maskfasta), or extract transcripts from a GFF (gffread). | draft | 2026-06-10 | 1 |
| Sequence: interconvert FASTA and tabular | Move sequence records between FASTA and a (header, sequence) table so tabular tools can edit them; fasta2tab one way, tab2fasta back. | draft | 2026-06-10 | 1 |
| Sequence: merge FASTA and filter unique | Concatenate several FASTA files into one and drop duplicate records by sequence identity in a single step; fasta_merge_files_and_filter_unique_sequences. | draft | 2026-06-10 | 1 |
| Sequence: reformat FASTA line width | Rewrap FASTA records to a fixed sequence-line width so downstream tools and viewers get canonical 60/70/80-column output; cshl_fasta_formatter. | draft | 2026-06-10 | 1 |
| Cleanup, sync, and publish non-empty results | Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results. | draft | 2026-05-04 | 1 |
| Fan-in bundle, consume, and flatten | Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing. | draft | 2026-05-04 | 1 |
| 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 | 2026-05-04 | 1 |
| Reshape, relabel, and remap by collection axis | Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis. | draft | 2026-05-04 | 1 |
| Collection: build list paired with Apply Rules | Use Apply Rules to promote identifier columns into a list:paired collection, with optional cleanup first. | draft | 2026-05-03 | 2 |
| Collection: build named bundle | Use BUILD_LIST to assemble named outputs into a collection bundle for publishing or downstream fan-in. | draft | 2026-05-03 | 2 |
| Collection: cleanup after map-over failure | Use FILTER_EMPTY or FILTER_FAILED after map-over when bad elements would break downstream collection steps. | draft | 2026-05-03 | 2 |
| Collection: flatten after fan-out | Use FLATTEN to collapse nested collection outputs to a flat list once the outer axis no longer matters. | draft | 2026-05-03 | 2 |
| Collection: split identifier via rules | Use Apply Rules regex columns to split one collection identifier into nested list identifiers. | draft | 2026-05-03 | 2 |
| Collection: swap nesting with Apply Rules | Use Apply Rules to regroup a list:list collection by swapping outer and inner identifier columns. | draft | 2026-05-03 | 2 |
| Collection: unbox singleton | Use __EXTRACT_DATASET__ with which: first when a one-element collection must become a dataset. | draft | 2026-05-03 | 2 |
| Parameter: compose runtime text parameter | Use compose_text_param to build connected text expressions from constants plus runtime scalar values. | draft | 2026-05-03 | 3 |
| 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 | 2026-05-03 | 3 |
| 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 | 2026-05-03 | 3 |
| Conditional: run optional step | Use a workflow boolean connected as inputs.when to skip an optional Galaxy step or branch. | draft | 2026-05-03 | 4 |
| Conditional: transform or pass through | Gate an optional transform, then use pick_value to pass transformed data when present or original data otherwise. | draft | 2026-05-03 | 2 |
| Parameter: derive from file | Read a one-value dataset with param_value_from_file, including count recipes that feed typed parameters. | draft | 2026-05-03 | 3 |
| Collection: harmonize by sortlist from identifiers | Use SORTLIST with sort_type:file to reorder one collection by another collection's identifiers. | draft | 2026-05-03 | 2 |
| Parameter: map workflow enum to tool parameter | Use map_param_value to translate workflow enum values into downstream tool codes, flags, or snippets. | draft | 2026-05-03 | 3 |
| Collection: regex relabel via tabular | Derive collection element identifiers in a tabular mapping, then apply them with RELABEL_FROM_FILE. | draft | 2026-05-03 | 2 |
| Collection: relabel via rules and find/replace | Use Apply Rules, identifier extraction, find/replace, and relabeling for structural fan-out cleanup. | draft | 2026-05-03 | 2 |
| Collection: sync collections by identifier | Use collection_element_identifiers with FILTER_FROM_FILE or RELABEL_FROM_FILE to align sibling collections. | draft | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 3 |
| 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 | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 2 |
| Tabular: filter rows by regex | Use tp_grep_tool for whole-line regex row filters on tabular input. Grep1 is the legacy alternative. | draft | 2026-05-03 | 2 |
| Tabular: group and aggregate | Use datamash_ops for grouped tabular aggregation: multi-column grouping, collapse, countunique, min/max, and reductions. | draft | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 2 |
| Tabular: prepend header | Use tp_awk_tool to prepend a constant header line, optionally skipping or reformatting an existing first row. | draft | 2026-05-03 | 2 |
| Tabular: relabel by row counter | Use tp_awk_tool to replace each row or label with deterministic sample_N values from awk NR. | draft | 2026-05-03 | 2 |
| Tabular: split taxonomy string | Use tp_awk_tool to split semicolon-delimited taxonomy strings into explicit rank columns with missing-rank handling. | draft | 2026-05-03 | 2 |
| Tabular: SQL query | Use query_tabular when SQL semantics justify it: windows, joins, anti-joins, or fused project+compute over tabulars. | draft | 2026-05-03 | 2 |
| 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 | 2026-05-03 | 2 |
| Tabular: to collection by row | Use split_file_to_collection split_by:col to fan a tabular into collection elements by row/key. | draft | 2026-05-03 | 2 |
| Galaxy: collection patterns | Use this MOC to choose corpus-grounded Galaxy collection transformation patterns. | draft | 2026-05-02 | 1 |
| Galaxy: conditionals patterns | Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns. | draft | 2026-05-02 | 1 |
| Galaxy: tabular patterns | Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns. | draft | 2026-05-02 | 1 |
Source Patterns (7)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| Nextflow: branch, filter, and ifEmpty to Galaxy filters and gates | Route Nextflow branch, filter, and ifEmpty channel idioms to Galaxy collection cleanup, identifier filters, when gates, or review. | draft | 2026-05-04 | 1 |
| Nextflow: grouped channel to regrouped Galaxy collection | Route Nextflow groupTuple, transpose, and grouped tuple payloads to Galaxy collection reshape patterns when the key is a real axis. | draft | 2026-05-04 | 1 |
| Nextflow: keyed join/combine(by:) to identifier-synchronized map-over | Route Nextflow keyed joins and combine(by:) pairings to Galaxy collection identifier sync, ordering, relabeling, or table joins. | draft | 2026-05-04 | 1 |
| Nextflow: mapped output cleanup and publishing | Route Nextflow mapped-output cleanup and publishDir-style intent to Galaxy filtering, relabeling, gating, bundling, and reports. | draft | 2026-05-04 | 1 |
| Nextflow: mix and collect to report aggregation | Route Nextflow mix, collect, toList, and collectFile report fan-in idioms to Galaxy aggregation and bundle patterns. | draft | 2026-05-04 | 1 |
| Nextflow: samplesheet rows to Galaxy collections | Route Nextflow samplesheet row streams and repeated tuple inputs to Galaxy list, paired, or list:paired collections. | draft | 2026-05-04 | 1 |
| Nextflow: source pattern map | Use this source-pattern map to route recurring Nextflow channel and operator idioms to Galaxy implementation patterns. | draft | 2026-05-03 | 1 |
CLI Commands (26)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| foundry validate-galaxy-tool-discovery | AJV gate for discover-shed-tool recommendation documents. | draft | 2026-08-04 | 2 |
| foundry validate-galaxy-tool-summary | AJV gate for galaxy-tool-cache summarize manifests, including the nested parsed_tool subtree. | draft | 2026-08-04 | 2 |
| foundry validate-galaxy-workflow-test-plan | AJV gate for Galaxy workflow test-plan YAML documents. | draft | 2026-08-04 | 2 |
| foundry validate-summary-cwl | AJV gate for summarize-cwl JSON documents. | draft | 2026-08-04 | 2 |
| foundry validate-summary-galaxy-workflow | AJV gate for summarize-galaxy-workflow JSON documents. | draft | 2026-08-04 | 2 |
| foundry validate-summary-nextflow | AJV gate for summarize-nextflow JSON documents. | draft | 2026-08-04 | 2 |
| galaxy-tool-cache add | Fetch a tool from the Tool Shed (shed-path or bare/stock id) and cache its ParsedTool locally for later summarize/schema. | draft | 2026-06-18 | 2 |
| galaxy-tool-cache list | Enumerate the tools in a cache directory with their resolved versions; the surface for confirming which stock/shed pin got cached. | draft | 2026-06-18 | 1 |
| galaxy-tool-cache summarize | Emit a deterministic galaxy-tool-summary manifest (cache provenance + embedded ParsedTool + generated input JSON Schemas) for a cached tool. | draft | 2026-06-18 | 2 |
| gxwf draft-extract | Extract the concrete subset of a draft workflow: trim drafty steps, strip `_plan_*`, promote class when fully resolved. | draft | 2026-05-27 | 1 |
| gxwf draft-next-step | Pick the next drafty step a harness should work on, or report no remaining work; deterministic topological + alphabetical tiebreak. | draft | 2026-05-27 | 1 |
| gxwf draft-validate | Validate a `class: GalaxyWorkflowDraft` workflow against draft-contract rules; with --concrete, also validate the extracted concrete subset. | draft | 2026-05-27 | 1 |
| foundry summarize-nextflow | Statically introspect a Nextflow / nf-core pipeline tree and emit a validated JSON summary. | draft | 2026-05-11 | 1 |
| foundry validate-tests-format | AJV gate for Galaxy workflow tests YAML, with optional workflow cross-check. | draft | 2026-05-11 | 1 |
| planemo cli_metadata | Export structured metadata for Planemo CLI commands. | draft | 2026-05-11 | 1 |
| planemo lint | Check for common errors and best practices. | draft | 2026-05-11 | 1 |
| planemo output_schema | Export JSON Schemas for Planemo machine-readable outputs. | draft | 2026-05-11 | 1 |
| planemo test | Run specified tool or workflow tests within Galaxy. | draft | 2026-05-11 | 1 |
| planemo workflow_test_init | Initialize a Galaxy workflow test description for supplied workflow. | draft | 2026-05-11 | 1 |
| planemo workflow_test_on_invocation | Run defined tests against existing workflow invocation. | draft | 2026-05-11 | 1 |
| gxwf convert | Convert a Galaxy workflow between native (.ga) and format2 (.gxwf.yml) representations. | draft | 2026-05-06 | 2 |
| gxwf tool-revisions | Resolve a Tool Shed tool to changeset revisions for reproducible workflow pinning. Final step in discover-and-pin. | draft | 2026-05-06 | 2 |
| gxwf tool-search | Free-text Tool Shed search returning candidate tools as JSON; first step in the discover-and-pin sequence. | draft | 2026-05-06 | 2 |
| gxwf tool-versions | List TRS-published versions of a Tool Shed tool, oldest→newest. Second step in the discover-and-pin sequence. | draft | 2026-05-06 | 2 |
| gxwf validate | Validate Galaxy workflow structure, tool state, and optional connection compatibility before runtime execution. | draft | 2026-05-06 | 3 |
| gxwf validate-tests | Validate Galaxy workflow test files and optionally cross-check labels against their workflow. | draft | 2026-05-06 | 3 |
Schemas (14)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| Cast provenance (_provenance.json, schema v4) | _provenance.json contract beside every cast: Mold revision, per-ref src/dst hashes, license lineage, artifact handoff. Schema v4 — deterministic casts only. | draft | 2026-08-04 | 3 |
| Galaxy workflow draft (gxformat2 superset) | JSON Schema for `class: GalaxyWorkflowDraft` — gxformat2 with `TODO_*` sentinels and `_plan_*` planning fields per draft step. | draft | 2026-08-03 | 2 |
| Planemo test report (JSON) | JSON Schema for the report emitted by `planemo test --test_output_json` (and friends), vendored from upstream planemo. | draft | 2026-07-20 | 3 |
| Galaxy workflow summary | JSON Schema for the structured summary emitted by the summarize-galaxy-workflow Mold. | draft | 2026-07-01 | 1 |
| Galaxy workflow test plan | JSON Schema for the intermediate Galaxy workflow test-plan handoff produced by the test-plan Molds and consumed by implement-galaxy-workflow-test. | draft | 2026-06-16 | 1 |
| CWL workflow summary | JSON Schema for the structured summary emitted by the summarize-cwl Mold. | draft | 2026-05-10 | 1 |
| Nextflow pipeline summary | JSON Schema for the structured summary emitted by the summarize-nextflow Mold. | draft | 2026-05-06 | 10 |
| Galaxy tool summary manifest | JSON Schema for the deterministic per-tool manifest emitted by `galaxy-tool-cache summarize`. | draft | 2026-05-05 | 1 |
| Nextflow parameter schema (nf-schema meta-schema) | JSON Schema (Draft 2020-12) meta-schema validating per-pipeline nextflow_schema.json files. Upstream from nextflow-io/nf-schema. | draft | 2026-05-05 | 1 |
| nf-core module meta.yml schema | JSON Schema (Draft-07) validating nf-core module meta.yml — channel IO, tools, containers, conda lockfiles. Upstream from nf-core/modules. | draft | 2026-05-05 | 1 |
| nf-core subworkflow meta.yml schema | JSON Schema (Draft-07) validating nf-core subworkflow meta.yml — channel IO, components dependencies, authors. Upstream from nf-core/modules. | draft | 2026-05-05 | 1 |
| Galaxy ParsedTool | JSON Schema for the upstream Galaxy `ParsedTool` model, vendored from `@galaxy-tool-util/schema`. | draft | 2026-05-05 | 1 |
| Galaxy workflow test format | JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`. | draft | 2026-05-05 | 4 |
| Galaxy tool discovery recommendation | JSON Schema for Tool Shed discovery hit, weak, and miss recommendations. | draft | 2026-05-04 | 1 |
Research (63)
| Name | Summary | Status | Revised | Rev |
|---|---|---|---|---|
| Component Nextflow Testing | nf-test patterns mapped to Galaxy planemo asserts and CWL test equivalents — backs the nextflow test-plan Molds and summarize-nextflow §7. | draft | 2026-08-03 | 3 |
| Alignment: gxy-sketches ↔ Galaxy Workflow Foundry | 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. | draft | 2026-07-24 | 2 |
| Open-requirements ledger | Carried unresolved-requirements artifact the source→Galaxy pipeline discharges or explicitly surrenders, autonomously. | draft | 2026-06-16 | 1 |
| Component Claude Dynamic Workflows | Dynamic workflows natively solve the per-step sub-DAG loop Archon couldn't, with schema-typed step handoffs; cost is in-session-only resume and no mid-run gate. | draft | 2026-06-15 | 1 |
| Galaxy Workflow Comments | How to annotate a gxformat2 workflow with editor comments: one titled frame per analysis stage, populate contains_steps, color decorative. | draft | 2026-06-12 | 1 |
| Iwc Comments Survey | How IWC uses the gxformat2 `comments:` array: titled stage frames dominate, color is decorative, frames travel with template forks. An authoring convention. | draft | 2026-06-12 | 1 |
| Galaxy <discover_datasets> | Reference for the <discover_datasets> Galaxy XML element — attributes, named/regex patterns, <data> vs <collection> contexts, test assertions. | draft | 2026-06-10 | 2 |
| Iwc Interval Operations Survey | IWC corpus survey of coordinate-aware genomic interval operations; sizing and candidate boundaries for a galaxy-interval-patterns MOC, with hold-if-thin gate. | draft | 2026-06-10 | 1 |
| Iwc Sequence Operations Survey | IWC survey of record-level FASTA manipulation (interconversion, reformat, merge/dedup, subset, extract-at-intervals); sizes a galaxy-sequence-patterns MOC. | draft | 2026-06-10 | 1 |
| 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 | 2026-06-10 | 3 |
| 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 | 2026-06-10 | 3 |
| 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. | draft | 2026-06-10 | 3 |
| 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 | 2026-06-10 | 3 |
| 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 | 2026-06-10 | 3 |
| Component Archon | Archon remains a heavy-harness candidate; HITL gates are stronger, but per-step sub-DAG looping is still the main gap. | draft | 2026-05-22 | 3 |
| CWL pickValue → Galaxy pick_value (post galaxy#22222) | CWL `pickValue` (first_non_null / the_only_non_null / all_non_null) → Galaxy's native `pick_value` workflow step added by galaxyproject/galaxy#22222. | draft | 2026-05-11 | 1 |
| CWL when:/pickValue → Galaxy branching translation | CWL `when:`/`pickValue` → Galaxy. Three honest translations (paired_or_unpaired input, native pick_value step, sibling workflows) plus how to pick among them. | draft | 2026-05-11 | 1 |
| Galaxy paired_or_unpaired collection type | Galaxy's `paired_or_unpaired` collection type: discriminated-union shape for paired-or-single reads, no workflow-level mode switch needed. Galaxy PR #19377. | draft | 2026-05-11 | 1 |
| Planemo Asserts Idioms | Decision and idiom guide for picking planemo workflow-test assertions: which family per output type, how to size tolerances, when to validate. | draft | 2026-05-11 | 6 |
| Planemo workflow-test architecture | Reference for Planemo workflow test/run architecture, Galaxy modes, API polling, and noisy failure boundaries. | draft | 2026-05-11 | 3 |
| CWL workflow anatomy | CWL structure relevant to summarize-cwl: normalized documents, steps, scatter, conditionals, requirements, and dependency handling. | draft | 2026-05-10 | 1 |
| CWL v1.2 schema documents | Vendored official CWL v1.2.1 JSON/SALAD schema documents used as source-structure reference for CWL summarization. | draft | 2026-05-10 | 1 |
| Galaxy workflow draft format | gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step. | draft | 2026-05-10 | 2 |
| Nextflow reference-data classification | Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact. | draft | 2026-05-10 | 3 |
| Nextflow to Galaxy reference-data mapping | Galaxy-side translation of Nextflow reference-data classifications: idioms available, the v1 posture, datatype defaults, and the in-tool rebuild trade-off. | draft | 2026-05-10 | 5 |
| Nextflow conditional to Galaxy subworkflow / when | Stub. Translate Nextflow conditionals into Galaxy `when:` (single-workflow v1). Subworkflow vs inline is an aesthetic call, not a rule. | draft | 2026-05-08 | 1 |
| Nextflow params to Galaxy workflow inputs | Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs. | draft | 2026-05-08 | 4 |
| Nextflow workflow I/O semantics | Defines Nextflow workflow inputs and outputs from docs plus observed fixture pipeline structures. | draft | 2026-05-08 | 4 |
| Galaxy datatypes registry sample | Vendored Galaxy datatypes registry sample: extension → datatype class mapping, sniff order, converters, and display applications. | draft | 2026-05-06 | 2 |
| Galaxy sample_sheet collection types | Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist. | draft | 2026-05-06 | 2 |
| Galaxy Workflow Testability Design | Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible. | draft | 2026-05-06 | 2 |
| gxformat2 structural JSON Schema | Vendored structural JSON Schema for gxformat2 workflows: vocabulary for inputs, outputs, steps, and step subtypes. | draft | 2026-05-06 | 2 |
| gxformat2 workflow inputs | Conceptual model, current aliases, and schema gaps for gxformat2 workflow inputs. | draft | 2026-05-06 | 2 |
| Nextflow path/glob to Galaxy datatype mapping | Rules for mapping Nextflow path, glob, sample-sheet, and output filename evidence to Galaxy datatype extensions. | draft | 2026-05-06 | 1 |
| Nextflow-to-Galaxy channel shape mapping | Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes. | draft | 2026-05-06 | 2 |
| nf-schema sample sheet validation gaps in Galaxy | nf-schema validation mapped to Galaxy column_definitions: what survives, degrades, or is lost; Galaxy work items + cast loss-recording vocabulary. | draft | 2026-05-06 | 1 |
| Component Nextflow Channel Operators | Structured digest of Nextflow channel operators (47 entries) with cardinality and shape semantics; backs summarize-nextflow §6 edge reconciliation. | draft | 2026-05-05 | 1 |
| Component Nextflow Containers And Envs | Container URL grammar (depot, BioContainers, mulled-v2, Wave, ORAS) and conda directive resolution rules backing summarize-nextflow §5. | draft | 2026-05-05 | 3 |
| Component Nf Core Module Conventions | RFC 2119 conventions enforced by nf-core/tools module lint, with lint-check pointers. Backs summarize-nextflow + author-galaxy-tool-wrapper. | draft | 2026-05-05 | 1 |
| Galaxy collection semantics | Vendored formal spec of Galaxy dataset-collection mapping/reduction semantics, with labeled examples and pinned test references. | draft | 2026-05-05 | 3 |
| Galaxy native workflow (.ga) structural JSON Schema | Vendored structural JSON Schema for Galaxy native workflow (.ga) format: vocabulary for the JSON shape Galaxy emits and consumes. | draft | 2026-05-05 | 1 |
| Galaxy tool XML schema | Vendored Galaxy tool XML schema for wrapper structure, parameters, outputs, tests, and assertion syntax. | draft | 2026-05-05 | 1 |
| Nextflow nf-test snapshots to Galaxy/Planemo assertions | Translates nf-test snapshot assertions into Galaxy workflow test-format assertions, broken out by module-level vs pipeline-level test shape. | draft | 2026-05-05 | 2 |
| Iwc Runtime Parameter Shims Survey | Focused survey of tiny IWC runtime parameter shims for flags, enums, counts, booleans, and composed text. | draft | 2026-05-04 | 1 |
| Component Tool Shed Search | Tool Shed's Whoosh repo/tool search and partial GA4GH TRS v2, indexed from hg-walked metadata with no auto-refresh on upload | draft | 2026-05-03 | 2 |
| Galaxy data-flow draft contract | Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation. | draft | 2026-05-03 | 2 |
| Galaxy tool summary input source | Decides that summarize-galaxy-tool reads cached ParsedTool JSON as its v1 input source. | draft | 2026-05-03 | 2 |
| Iwc Map Over Lifecycle Survey | Survey of IWC map-over lifecycle recipes, with a Nextflow-to-Galaxy crosswalk for collection construction, cleanup, reshape, reduce, and publish phases. | draft | 2026-05-03 | 1 |
| Iwc Shortcuts Anti Patterns | 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. | draft | 2026-05-03 | 2 |
| Iwc Test Data Conventions | How IWC workflows organize and reference test data — Zenodo-first, SHA-1 integrity, collection shapes, CVMFS gotchas. | draft | 2026-05-03 | 3 |
| Iwc Workflow Testability Survey | IWC evidence survey for Galaxy workflow structures that make workflow tests meaningful. | draft | 2026-05-03 | 2 |
| Galaxy Apply Rules DSL | Reference for Galaxy's Apply Rules DSL: rule operations, mapping operations, composition patterns, pitfalls. | draft | 2026-05-02 | 2 |
| Galaxy collection-operation tools | Catalog of Galaxy's collection-operation tools — purpose, IO, parameters, selection guide. Companion to galaxy-collection-semantics. | draft | 2026-05-02 | 2 |
| Galaxy tool and job failure reference | Reference for Galaxy tool stdio rules, job failure detection, job states, and job API failure surfaces. | draft | 2026-05-02 | 1 |
| Galaxy workflow invocation failure reference | Reference for Galaxy workflow invocation states, messages, failure reasons, and invocation API surfaces. | draft | 2026-05-02 | 1 |
| Iwc Conditionals Survey | Corpus survey of Galaxy conditional step usage in IWC, covering when-gates, boolean shims, and routed output selection. | draft | 2026-05-02 | 2 |
| Iwc Parameter Derivation Survey | Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters. | draft | 2026-05-02 | 1 |
| Iwc Tabular Operations Survey | Corpus survey of tabular tools and operations across IWC workflows; map for the operation pattern hierarchy on row/column data manipulation. | draft | 2026-05-02 | 2 |
| Iwc Transformations Survey | Corpus survey of collection-shape transformations across IWC: built-in collection ops, toolshed transformers, and the multi-step recipes that bracket map-over. | draft | 2026-05-02 | 2 |
| Nextflow operators to Galaxy collection recipes | Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers. | draft | 2026-05-02 | 1 |
| Component Nextflow Inspect | White paper on Nextflow's native introspection subcommands — `nextflow inspect`, `nextflow config`, and adjacent tooling. Survey, not decision. | draft | 2026-05-01 | 1 |
| Component Nextflow Pipeline Anatomy | Stub. DSL2 layout, channel idioms, operator-chain reading rules. Grows from cast contact with rnaseq/sarek/ad-hoc — see issue #17. | draft | 2026-05-01 | 1 |
| Component Nf Core Tools | White paper on nf-core/tools — conventions, CLI surface, schema universe, container resolution. Survey, not decision. | draft | 2026-05-01 | 1 |
Project Infrastructure Research (7)
| Name | Summary | Surface |
|---|---|---|
| Comparisons | Where the Foundry sits versus wikis, skill bundles, and the KB-to-skill landscape (MCP, Agent Skills, llms.txt, Corpus2Skill, RAG) — a dated snapshot. | design |
| Pattern Authorship Policy | Developer-facing authorship rules for operation-named, corpus-grounded pattern pages. | design |
| Schema Packages | Where a Mold IO schema lives, how cast resolves one through a schema note, and why there is no separate schema package. | design |
| Code Architecture | Implementation components, dependency direction, entry points, and contracts across the Foundry codebase. | design |
| Content Model | How Foundry notes, kinds, metadata, tags, links, references, and companions represent knowledge. | design |
| Build and Validation | How authored Foundry source is checked, generated, cast, assembled, rendered, and kept current. | design |
| Repository Layout | Where authored source, implementation code, generated artifacts, fixtures, and site files belong. | design |