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EOAP CWL Wrap

eoap-cwlwrap is a command-line utility that composes a CWL Workflow from a series of Workflow/CommandLineTool steps, defined according to Application package patterns based on data stage-in and stage-out behaviors commonly used in EO workflows, and packs it into a single self-contained CWL document.

🛠 Installation

pip install eoap-cwlwrap

or, for early adopters:

pip install --no-cache-dir git+https://github.com/EOEPCA/eoap-cwlwrap@main

🧠 Prerequisites

stage-in

  • One input parameter of type URI;
  • One output of type Directory.

stage-out

  • One input parameter of type Directory;
  • One output of type URI.

app

Inputs:

  • has one or more parameter of type Directory or File, that:
    • it can be nullable ?;
    • it can be an array [].

Outputs:

  • has one or more parameter of type Directory
    • it can be an array [].

main

  • inputs coming from app:
    • if type is assignable to Directory or File, it is converted to URI input in main;
    • any other kind of input won't be transformed;
  • outpus coming from app:
    • if type is assignable to Directory it is converted to URI output in main;
    • any other kind of output won't be transformed, but referenced to the related app output;

🚀 Features

  • 🧱 Chain multiple Workflow/CommandLineTool CWLs into a Workflow;
  • 🧪 Validate type compatibility between steps;
  • 📦 Pack the entire workflow and dependencies into one file;
  • 💾 Output to any location, with automatic directory creation.

🧑‍💻 Usage

eoap-cwlwrap \
--stage-in ./stage-in.cwl \
--workflow ./workflow.cwl \
--workflow-id water-bodies-detection \
--stage-out ./stage-out.cwl \
--output ./current.cwl

🔧 Options

Option Description
--directory-stage-in The CWL stage-in URL or file for Directory derived types
--file-stage-in The CWL stage-in URL or file for File derived types
--workflow The CWL workflow URL or file
--workflow-id ID of the workflow
--stage-out `The CWL stage-out URL or file
--output" The output file path

🧠 Requirements

  • Python ≥ 3.9

Dependendies

Package installation will automatically install the following dependencies:

Using the container

docker run -it --rm ghcr.io/eoepca/eoap-cwlwrap/eoap-cwlwrap:latest eoap-cwlwrap --help

Run the tests

hatch test --verbose