cwltool Direct

Run cwltool on your machine without an orchestration container. cwltool will still use Docker (or Singularity) to run the individual tool containers.

Prerequisites

• Python 3 with pip
• cwltool: pip install cwltool
• Docker (for tool containers)

Windows Users

CWL requires a Unix-like environment. Use WSL (Windows Subsystem for Linux):

1. Install WSL: wsl --install (then restart)
2. In WSL: sudo apt update && sudo apt install python3 python3-pip
3. pip install cwltool

1. Unzip

unzip my_pipeline.crate.zip -d my_workflow
cd my_workflow
chmod +x workflows/*.cwl run.sh run_singularity.sh prefetch_images.sh prefetch_images_singularity.sh

2. Edit the Job File

Open workflows/<name>_job.yml and replace file path placeholders with your actual data paths.

3. Run

cwltool workflows/<name>.cwl workflows/<name>_job.yml

With a specific output directory:

cwltool --outdir ./results workflows/<name>.cwl workflows/<name>_job.yml