cwl-runner 命令

常用示例

说明

cwl-runner executes workflows defined in Common Workflow Language (CWL), a specification for describing analysis workflows in data-intensive sciences. CWL workflows are portable across different execution environments. The runner takes a CWL document and input parameters, resolves dependencies, and executes tools in the correct order. Steps can be run in containers (Docker/Singularity) for reproducibility, or natively if tools are installed locally. Input parameters can be specified in a YAML/JSON file or as command-line arguments. Outputs are placed in the specified output directory with a manifest describing the results.

参数

--validate

Validate the CWL document without running.

--outdir _path_

Output directory for results.

--no-container

Disable Docker/container execution.

--parallel

Run workflow steps in parallel.

--cachedir _path_

Directory for caching intermediate results.

--tmpdir-prefix _path_

Prefix for temporary directories.

--debug

Enable debug output.

--quiet

Only print warnings and errors.

--validate

Validate the CWL document without running.

--leave-tmpdir

Don't delete temporary directories.

--version

Print version and exit.

--make-template

Generate template input object.

--on-error _action_

Workflow behavior on failure (stop or continue).

--singularity

Use Singularity container runtime instead of Docker.

--podman

Use Podman container runtime instead of Docker.