foundry-skills

Plugin foundry-skills from marketplace galaxy-workflow-foundry in galaxyproject/foundry. Commands read from the repo's manifest — today.

Skills (69)

• advance-galaxy-draft-step

  Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.

• apply-galaxy-workflow-changeset

  Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.

• author-galaxy-tool-wrapper

  Author a new Galaxy user-defined tool YAML definition when Tool Shed discovery misses.

• 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.

• compare-against-iwc-exemplar

  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

  Convert one nf-core module directory into a Galaxy wrapper with local macros, provenance, and remote fixture-backed tests.

• cwl-summary-to-galaxy-data-flow

  Translate a CWL summary into a Galaxy data-flow design brief.

• cwl-summary-to-galaxy-interface

  Map a CWL summary into a Galaxy workflow interface design brief.

• cwl-summary-to-galaxy-template

  gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.

• cwl-test-to-galaxy-test-plan

  Translate CWL test fixtures into a Galaxy workflow test plan.

• cwl-to-test-data

  Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs.

• debug-cwl-workflow-output

  Triage failing CWL run outputs; classify failure modes; propose fixes.

• debug-galaxy-workflow-output

  Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.

• 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.

• find-test-data

  Search IWC fixtures and public sources for test data matching a data-flow shape.

• freeform-summary-to-cwl-design

  Translate a free-form source summary into a CWL workflow design brief.

• freeform-summary-to-galaxy-data-flow

  Translate a free-form source summary into a Galaxy data-flow design brief.

• freeform-summary-to-galaxy-interface

  Map a free-form source summary into a Galaxy workflow interface design brief.

• freeform-summary-to-galaxy-template

  gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.

• freeform-summary-to-galaxy-test-plan

  Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.

• freeform-summary-to-workflow-brief

  Turn a freeform source summary and selected scope into a Workflow Brief without Galaxy design assumptions.

• implement-cwl-tool-step

  Convert an abstract step into a concrete CWL CommandLineTool + step.

• implement-cwl-workflow-test

  Assemble CWL job file(s) and expected-output assertions.

• implement-galaxy-tool-step

  Convert an abstract step into a concrete gxformat2 step using a tool summary or an authored user-defined tool.

• implement-galaxy-workflow-test

  Assemble Galaxy workflow test fixtures and assertions.

• interview-to-freeform-summary

  Normalize a free-form user interview into the shared freeform-summary workflow handoff.

• interview-to-galaxy-workflow-changeset

  Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.

• mature-galaxy-workflow-for-iwc

  Apply the IWC publication checklist to an existing Galaxy workflow and emit a generalized, reviewable submission set.

• nextflow-summary-to-cwl-data-flow

  Translate a Nextflow summary into a CWL data-flow design brief.

• nextflow-summary-to-cwl-interface

  Map a Nextflow summary into a CWL Workflow interface design brief.

• nextflow-summary-to-galaxy-data-flow

  Translate a Nextflow summary into a Galaxy data-flow design brief.

• nextflow-summary-to-galaxy-interface

  Map a Nextflow summary into a Galaxy workflow interface design brief.

• nextflow-summary-to-galaxy-reference-data

  Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.

• nextflow-summary-to-galaxy-template

  gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.

• nextflow-summary-to-workflow-brief

  Turn a nextflow source summary and selected scope into a Workflow Brief without Galaxy design assumptions.

• nextflow-test-to-cwl-test-plan

  Translate Nextflow test evidence into a CWL workflow test plan.

• nextflow-test-to-galaxy-test-plan

  Translate Nextflow test evidence into a Galaxy workflow test plan.

• nextflow-to-test-data

  Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.

• paper-to-test-data

  Resolve the test data a paper names into refs for each workflow input.

• pipeline-cwl-to-galaxy

  Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test — orchestrates the Foundry skills of the CWL → GALAXY pipeline in order, in a per-run working directory.

• pipeline-galaxy-workflow-maturation

  Apply the pinned IWC publication checklist to an existing Galaxy workflow, then validate and retest the matured result — orchestrates the Foundry skills of the GALAXY WORKFLOW MATURATION pipeline in order, in a per-run working directory.

• pipeline-galaxy-workflow-review

  Post-construction review journey: summarize, validate, and test an existing Galaxy workflow, then apply pinned IWC policy — orchestrates the Foundry skills of the GALAXY WORKFLOW REVIEW pipeline in order, in a per-run working directory.

• pipeline-interview-to-galaxy

  Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff — orchestrates the Foundry skills of the INTERVIEW → GALAXY pipeline in order, in a per-run working directory.

• pipeline-interview-to-workflow-brief

  Summarize an interview source and produce a scoped Workflow Brief for expert review — orchestrates the Foundry skills of the INTERVIEW → WORKFLOW BRIEF pipeline in order, in a per-run working directory.

• pipeline-nextflow-to-cwl

  Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set — orchestrates the Foundry skills of the NEXTFLOW → CWL pipeline in order, in a per-run working directory.

• pipeline-nextflow-to-galaxy

  Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the NEXTFLOW → GALAXY pipeline in order, in a per-run working directory.

• pipeline-nextflow-to-workflow-brief

  Summarize a Nextflow pipeline and produce a scoped Workflow Brief for expert review — orchestrates the Foundry skills of the NEXTFLOW → WORKFLOW BRIEF pipeline in order, in a per-run working directory.

• pipeline-paper-to-cwl

  Direct path from a paper to a CWL Workflow + CommandLineTool set — orchestrates the Foundry skills of the PAPER → CWL pipeline in order, in a per-run working directory.

• pipeline-paper-to-galaxy

  Direct path from a paper to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the PAPER → GALAXY pipeline in order, in a per-run working directory.

• pipeline-paper-to-workflow-brief

  Summarize a paper source and produce a scoped Workflow Brief for expert review — orchestrates the Foundry skills of the PAPER → WORKFLOW BRIEF pipeline in order, in a per-run working directory.

• pipeline-update-interview-to-galaxy

  Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop — orchestrates the Foundry skills of the UPDATE-INTERVIEW → GALAXY pipeline in order, in a per-run working directory.

• pipeline-workflow-brief-to-galaxy

  Consume an expert-reviewed, unchanged Workflow Brief directly through the Galaxy design and implementation chain — orchestrates the Foundry skills of the WORKFLOW BRIEF → GALAXY pipeline in order, in a per-run working directory.

• repair-galaxy-draft-topology

  Make the smallest structural edit that closes an open blocking entry in a settled Galaxy draft.

• report-foundry-run-feedback

  Triage a completed or partial Foundry feedback ledger into a run review and confirmed, deduplicated upstream issue drafts.

• review-galaxy-workflow

  Apply the pinned upstream IWC review policy to one Galaxy workflow or pull request and emit one evidenced advisory Markdown review.

• run-workflow-test

  Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.

• summarize-cwl-tool

  Derive a CommandLineTool description (container, baseCommand, IO) for a CWL target.

• summarize-cwl

  Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.

• summarize-galaxy-tool

  Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.

• summarize-galaxy-workflow

  Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.

• summarize-nextflow

  Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds.

• summarize-paper

  Extract methods, tools, sample data, and references from a paper.

• summary-to-cwl-template

  CWL Workflow skeleton with per-step TODOs from source and design handoffs.

• validate-cwl

  Run cwltool --validate / schema lint, classify failures, recommend fixes.

• validate-galaxy-workflow

  Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.

• workflow-brief-to-galaxy-data-flow

  Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.

• workflow-brief-to-galaxy-interface

  Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.

• workflow-brief-to-galaxy-template

  Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.

• workflow-brief-to-galaxy-test-plan

  Synthesize a Galaxy workflow test plan from a reviewed Workflow Brief, its Galaxy design briefs, and available source evidence.

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