reviewed galaxy
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.
Source artifacts for casting.
Molds are atomic action templates grouped by axis, then cast into target-specific skills and harness steps.
- Total
- 56
- Axes
- 3
- Eval Plans
- 42/56
source-specific
/ 30 molds draft cwl
cwl-summary-to-galaxy-data-flow
Translate a CWL summary into a Galaxy data-flow design brief.
draft cwl
cwl-summary-to-galaxy-interface
Map a CWL summary into a Galaxy workflow interface design brief.
draft cwl
cwl-summary-to-galaxy-template
gxformat2 skeleton with per-step TODOs from a CWL summary and prior Galaxy design briefs.
draft cwl
cwl-test-to-galaxy-test-plan
Translate CWL test fixtures into a Galaxy workflow test plan.
draft cwl
cwl-to-test-data
Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs.
draft freeform
freeform-summary-to-cwl-design
Translate a free-form source summary into a CWL workflow design brief.
reviewed freeform
freeform-summary-to-galaxy-data-flow
Translate a free-form source summary into a Galaxy data-flow design brief.
reviewed freeform
freeform-summary-to-galaxy-interface
Map a free-form source summary into a Galaxy workflow interface design brief.
reviewed freeform
freeform-summary-to-galaxy-template
gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.
reviewed freeform
freeform-summary-to-galaxy-test-plan
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
draft freeform
freeform-summary-to-workflow-brief
Turn a freeform source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
reviewed interview
interview-to-freeform-summary
Normalize a free-form user interview into the shared freeform-summary workflow handoff.
reviewed interview
interview-to-galaxy-workflow-changeset
Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.
draft nextflow
nextflow-summary-to-cwl-data-flow
Translate a Nextflow summary into a CWL data-flow design brief.
draft nextflow
nextflow-summary-to-cwl-interface
Map a Nextflow summary into a CWL Workflow interface design brief.
reviewed nextflow
nextflow-summary-to-galaxy-data-flow
Translate a Nextflow summary into a Galaxy data-flow design brief.
reviewed nextflow
nextflow-summary-to-galaxy-interface
Map a Nextflow summary into a Galaxy workflow interface design brief.
reviewed nextflow
nextflow-summary-to-galaxy-reference-data
Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
reviewed nextflow
nextflow-summary-to-galaxy-template
gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
draft nextflow
nextflow-summary-to-workflow-brief
Turn a nextflow source summary and selected scope into a Workflow Brief without Galaxy design assumptions.
draft nextflow
nextflow-test-to-cwl-test-plan
Translate Nextflow test evidence into a CWL workflow test plan.
reviewed nextflow
nextflow-test-to-galaxy-test-plan
Translate Nextflow test evidence into a Galaxy workflow test plan.
reviewed nextflow
nextflow-to-test-data
Resolve a Nextflow pipeline's own declared test fixtures into Galaxy workflow test-data refs.
draft paper
paper-to-test-data
Resolve the test data a paper names into refs for each workflow input.
draft galaxy
review-galaxy-workflow
Apply the pinned upstream IWC review policy to one Galaxy workflow or pull request and emit one evidenced advisory Markdown review.
draft cwl
summarize-cwl
Validate and normalize a CWL Workflow tree, then emit a lightweight structured summary for downstream Galaxy translation.
reviewed galaxy
summarize-galaxy-workflow
Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.
reviewed nextflow
summarize-nextflow
Read a Nextflow pipeline source tree (nf-core or ad-hoc DSL2) and emit a structured JSON summary for downstream translation Molds.
draft paper
summarize-paper
Extract methods, tools, sample data, and references from a paper.
target-specific
/ 23 molds reviewed galaxy
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 galaxy
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 galaxy
author-galaxy-tool-wrapper
Author a new Galaxy user-defined tool YAML definition when discovery yields nothing acceptable.
reviewed galaxy
compare-against-iwc-exemplar
Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.
draft galaxy
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.
draft cwl
debug-cwl-workflow-output
Triage failing CWL run outputs; classify failure modes; propose fixes.
reviewed galaxy
debug-galaxy-workflow-output
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
reviewed galaxy
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.
draft cwl
implement-cwl-tool-step
Convert an abstract step into a concrete CWL CommandLineTool + step.
draft cwl
implement-cwl-workflow-test
Assemble CWL job file(s) and expected-output assertions.
reviewed galaxy
implement-galaxy-tool-step
Convert an abstract step into a concrete gxformat2 step using a tool summary.
reviewed galaxy
implement-galaxy-workflow-test
Assemble Galaxy workflow test fixtures and assertions.
draft galaxy
mature-galaxy-workflow-for-iwc
Apply the IWC publication checklist to an existing Galaxy workflow and emit a generalized, reviewable submission set.
draft galaxy
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 cwl
summarize-cwl-tool
Derive a CommandLineTool description (container, baseCommand, IO) for a CWL target.
reviewed galaxy
summarize-galaxy-tool
Pull JSON schema, container, source, inputs/outputs for a Galaxy tool.
draft cwl
summary-to-cwl-template
CWL Workflow skeleton with per-step TODOs from source and design handoffs.
draft cwl
validate-cwl
Run cwltool --validate / schema lint, classify failures, recommend fixes.
reviewed galaxy
validate-galaxy-workflow
Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.
draft galaxy
workflow-brief-to-galaxy-data-flow
Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.
draft galaxy
workflow-brief-to-galaxy-interface
Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.
draft galaxy
workflow-brief-to-galaxy-template
Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.
draft galaxy
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.
generic
/ 3 molds reviewed
find-test-data
Search IWC fixtures and public sources for test data matching a data-flow shape.
draft
report-foundry-run-feedback
Triage a completed or partial Foundry feedback ledger into a run review and confirmed, deduplicated upstream issue drafts.
reviewed
run-workflow-test
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.