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YAML Workflow Reference

Workflows let you chain MedCheck steps into reproducible pipelines defined in a single YAML file. Place workflow files anywhere under the workflows/ directory.

File format

name: string          # required — unique workflow identifier
description: string   # optional
steps:
  - id: string        # required — unique step identifier within this workflow
    uses: string      # required — step type (see Available Steps below)
    with:             # optional — step-specific configuration
      key: value
    depends_on:       # optional — list of step ids that must complete first
      - other_step_id

Available steps

load

Load images from a source.

Option Type Default Description
source string — File path, URL, or PACS reference
anatomy string null Anatomy hint (knee, shoulder, spine)

preprocess

Apply standard MRI preprocessing.

Option Type Default Description
normalize bool true Intensity normalization
denoise bool false Apply denoising filter
slice_select string "all" Slice selection strategy

analyze

Run LLM-based structural analysis.

Option Type Default Description
model string "claude-opus-4-8" LLM to use
anatomy string — Anatomy region (required if not set in load)
prompt_override string null Path to a custom system prompt

validate

Validate the analysis output against report_schema.json.

Option Type Default Description
strict bool false Fail the workflow on schema violations

report

Generate a human-readable report.

Option Type Default Description
format string "json" Output format: json, pdf, html
output string "output/" Destination directory or file path

Examples

Basic knee analysis

name: knee-basic
description: Single-file knee MRI analysis with PDF report

steps:
  - id: load
    uses: load
    with:
      source: data/knee_001.dcm
      anatomy: knee

  - id: analyze
    uses: analyze
    depends_on: [load]
    with:
      model: claude-opus-4-8

  - id: report
    uses: report
    depends_on: [analyze]
    with:
      format: pdf
      output: output/knee_001_report.pdf

Batch portal analysis

name: batch-shoulder
description: Pull studies from portal and analyze in parallel

steps:
  - id: load
    uses: load
    with:
      source: https://portal.example.com/study/${STUDY_ID}
      anatomy: shoulder

  - id: preprocess
    uses: preprocess
    depends_on: [load]
    with:
      normalize: true
      denoise: true

  - id: analyze
    uses: analyze
    depends_on: [preprocess]
    with:
      model: gemini-3-5-flash

  - id: validate
    uses: validate
    depends_on: [analyze]
    with:
      strict: true

  - id: report
    uses: report
    depends_on: [validate]
    with:
      format: html
      output: output/