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Start Pipeline

start_pipeline

Launch all six Champollion pipeline stages sequentially and get a job ID for tracking, enabling a full MRI-to-sulcal-embedding run without manual stage calls.

Instructions

Launch the full Champollion pipeline (all 6 stages sequentially). Returns a pipeline job_id immediately.

reference_data_dir is optional and forwarded to stage 6 (snapshots) for UMAP plots.

A non-empty masks is forwarded to stages 2, 3 and 4, and names the <datasets_root>/derivatives/champollion_V1/<masks or canonical_25>/ directory that stages 5 and 6 read and write (region_embeddings, embeddings, snapshots). overwrite, run_cka, regions, masks_version and cortical_version apply to stage 4 (embeddings) only. regions are model names (e.g. SCsylv_left); cortical_version must name where the stage-2 crops actually are.

Input Schema

NameRequiredDescriptionDefault
cpuNo
masksNo
njobsNo
datasetYes
regionsNo
run_ckaNo
parallelNo
crop_pathYes
input_dirYes
overwriteNo
output_dirYes
sk_qc_pathNo
models_pathYes
skip_stagesNo
datasets_rootYes
masks_versionNo
path_to_graphYes
cortical_versionNo
labelling_sessionNo
path_sk_with_hullYes
reference_data_dirNo

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

B3.4/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden. It usefully discloses async behavior ("Returns a pipeline job_id immediately") and which stages read/write the masks directory, but omits failure behavior, whether overwrite can destroy existing data, and how this job interacts with cancel_job/get_job_status.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loads purpose and return in the first sentence, then groups parameter behavior by stage. Dense but earned for a 21-parameter tool; only minor tightening is possible.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be explained, and the job_id is still noted. However, for a 21-parameter, zero-coverage, no-annotation mutation tool, the description leaves too many required inputs and the skip_stages option undocumented to be considered complete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0% across 21 parameters, so the description must compensate and only partially does. It adds real meaning for masks, reference_data_dir, overwrite, run_cka, regions, masks_version, and cortical_version, but leaves the 8 required paths plus cpu, njobs, parallel, skip_stages, and labelling_session entirely undefined — skip_stages in particular is never mentioned.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ("Launch the full Champollion pipeline"), quantifies scope ("all 6 stages sequentially"), and discloses the immediate return (job_id). It implicitly distinguishes itself from the stage-level siblings via "full" and "all 6 stages," but never names an alternative tool, so it stops short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is implied rather than stated: the pipeline runs everything, so an agent can infer the stage-level siblings (start_embeddings, start_snapshots, etc.) are for partial runs, but the description never says when to prefer start_pipeline over them. No prerequisites or exclusions are given.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.