cwl_utils.docker_extract

Functions

arg_parser()	Argument parser.
run(args)	Extract the docker reqs and download them using Singularity or Docker.
extract_docker_requirements(process)	Yield an iterator of the docker reqs, normalizing the pull request.
extract_docker_reqs(process)	For the given process, extract the DockerRequirement(s).
traverse(process)	Yield the iterator for the docker reqs, including an workflow steps.
get_process_from_step(step)	Return the process for this step, loading it if necessary.
traverse_workflow(workflow)	Iterate over the steps of this workflow, yielding the docker reqs.
main()	Command line entry point.

Module Contents

cwl_utils.docker_extract.arg_parser()

Argument parser.

Return type:

argparse.ArgumentParser

cwl_utils.docker_extract.run(args)

Extract the docker reqs and download them using Singularity or Docker.

Parameters:

args (argparse.Namespace)

Return type:

list[cwl_utils.parser.DockerRequirement]

cwl_utils.docker_extract.extract_docker_requirements(process)

Yield an iterator of the docker reqs, normalizing the pull request.

Parameters:

process (cwl_utils.parser.Process)

Return type:

collections.abc.Iterator[cwl_utils.parser.DockerRequirement]

cwl_utils.docker_extract.extract_docker_reqs(process)

For the given process, extract the DockerRequirement(s).

Parameters:

process (cwl_utils.parser.Process)

Return type:

collections.abc.Iterator[cwl_utils.parser.DockerRequirement]

cwl_utils.docker_extract.traverse(process)

Yield the iterator for the docker reqs, including an workflow steps.

Parameters:

process (cwl_utils.parser.Process)

Return type:

collections.abc.Iterator[cwl_utils.parser.DockerRequirement]

cwl_utils.docker_extract.get_process_from_step(step)

Return the process for this step, loading it if necessary.

Parameters:

step (cwl_utils.parser.WorkflowStep)

Return type:

cwl_utils.parser.Process

cwl_utils.docker_extract.traverse_workflow(workflow)

Iterate over the steps of this workflow, yielding the docker reqs.

Parameters:

workflow (cwl_utils.parser.Workflow)

Return type:

collections.abc.Iterator[cwl_utils.parser.DockerRequirement]

cwl_utils.docker_extract.main()

Command line entry point.

Return type:

int