Transpile a CWL Workflow to a Markdown page

The main purpose of this command is having a human-readable visual representation of a CWL Workflow:

$ transpiler-mate markdown --help
Usage: transpiler-mate markdown [OPTIONS] SOURCE

  Transpiles the input CWL to Markdown documentation.

Options:
  --workflow-id TEXT      ID of the main Workflow  [default: main; required]
  --output PATH           The output directory path  [default: .]
  --code-repository TEXT  The (SVN, GitHub, CodePlex, ...) code repository URL
  --help                  Show this message and exit.

i.e.

$ transpiler-mate markdown \
--workflow-id ml4floods \
--output ./test/ \
--code-repository `git remote get-url origin` \
~/Documents/app-ml4floods-0.2.0.cwl

2026-01-22 16:32:29.846 | INFO     | transpiler_mate.cli:markdown:304 - Rendering Markdown documentation of ~/Documents/app-ml4floods-0.2.0.cwl to test/ml4floods.md...
2026-01-22 16:32:29.846 | INFO     | transpiler_mate.markdown:markdown_transpile:233 - Reading metadata from ~/Documents/app-ml4floods-0.2.0.cwl...
2026-01-22 16:32:29.846 | DEBUG    | transpiler_mate.metadata:__init__:62 - Loading raw document from ~/Documents/app-ml4floods-0.2.0.cwl...
2026-01-22 16:32:29.958 | INFO     | transpiler_mate.metadata:__init__:78 - Resolving License details from SPDX License List...
2026-01-22 16:32:29.958 | INFO     | transpiler_mate.metadata:resolve_license:82 - Detected CC-BY-4.0 indexed in SPDX Licenses
2026-01-22 16:32:29.958 | SUCCESS  | transpiler_mate.markdown:markdown_transpile:236 - Metadata successfully read!
2026-01-22 16:32:29.958 | INFO     | transpiler_mate.markdown:markdown_transpile:237 - Transpiling metadata...
2026-01-22 16:32:29.960 | SUCCESS  | transpiler_mate.markdown:markdown_transpile:242 - Metadata successfully transpiled!
2026-01-22 16:32:29.960 | INFO     | transpiler_mate.markdown:markdown_transpile:243 - Reading Workflow model...
2026-01-22 16:32:29.960 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - No needs to update the Raw CWL document since it targets already the v1.2
2026-01-22 16:32:29.960 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:_on_process:78 - Checking if #ml4floods-cli must be externally imported...
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:_on_process:82 - run_url:  - uri: io://
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable! 
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....
2026-01-22 16:32:29.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.
2026-01-22 16:32:29.963 | SUCCESS  | transpiler_mate.markdown:markdown_transpile:251 - Workflow model successfully read!
2026-01-22 16:32:29.983 | INFO     | transpiler_mate.cli:markdown:314 - Markdown documentation successfully serialized to test/ml4floods.md!

It is strongly recommended to use this command combined with the cwl2puml CLI tool, to render the Workflow, i.e.

cwl2puml \
--workflow-id ml4floods \
--output ./test/ \
--convert-image \
--image-format svg \
~/Documents/app-ml4floods-0.2.0.cwl

The page will look alike the produced documentation below

---

ML4Floods inference for flood extent estimation using pre-trained model on Sentinel-2 or Landsat-9 data v0.2.0

ML4Floods is an end-to-end ML pipeline for flood extent estimation using optical satellite data from Sentinel-2 or Landsat-8/9 acquisition

This software is licensed under the terms of the Creative Commons Attribution 4.0 International license - SPDX short identifier: CC-BY-4.0

2025-10-29 - 2026-01-22T16:32:29.966 Copyright Terradue Srl - > https://ror.org/0069cx113

Project Team

Authors

Name	Email	Organization	Role	Identifier
Brito, Fabrice	fabrice.brito@terradue.com	Terradue	Project Manager	https://orcid.org/0009-0000-1342-9736
Re, Alice	alice.re@terradue.com	Terradue	Researcher	https://orcid.org/0000-0001-7068-5533
Tripodi, Simone	simone.tripodi@terradue.com	Terradue	Project Leader	https://orcid.org/0009-0006-2063-618X

Contributors

Name	Email	Organization	Role	Identifier
Vaccari, Simone	simone.vaccari@terradue.com	Terradue	Researcher	https://orcid.org/0000-0002-2757-4165

User Manual

User Manual can be found on https://eoap.github.io/app-ml4floods/.

Runtime environment

Supported Operating Systems

• Linux
• MacOS X

Requirements

• https://cwltool.readthedocs.io/en/latest/
• https://www.python.org/

Software Source code

• Browsable version of the source repository;
• Continuous integration system used by the project;
• Issues, bugs, and feature requests should be submitted to the following issue management system for this project

---

Workflow

ml4floods

CWL Class

Workflow

Inputs

Id	Type	Label	Doc
input-item	string	Optical satellite acquisition	Sentinel-2 or Landsat-9 acquisition to be processed
water-threshold	[ null, float ]	Water threshold	Threshold for water detection (default 0.7)
brightness-threshold	[ null, int ]	Brightness threshold	Threshold for brightness (default 3500)

Steps

Id	Runs	Label	Doc
inference	#ml4floods-cli	None	None

Outputs

Id	Type	Label	Doc
flood-delineation	Directory	None	None

UML Diagrams

UML activity diagram

UML component diagram

UML class diagram

UML sequence diagram

UML state diagram

ml4floods-cli

CWL Class

CommandLineTool

Inputs

Id	Option	Type
input_item	--input-item	string
water_threshold	--water-threshold	[ null, float ]
brightness_threshold	--brightness-threshold	[ null, int ]

Execution usage example:

ml4floods-cli \
--input-item <INPUT_ITEM> \
(--water-threshold <WATER_THRESHOLD>) \
(--brightness-threshold <BRIGHTNESS_THRESHOLD>)

Run in step

inference