API Documentation

pype
pype.utils
pype.process
pype.misc
pype.logger
pype.exceptions	Central exception handling for bio_pype.

Core Components

Pipeline Management

Pipeline
PipelineItem
get_pipelines	Get all available pipelines and add them to parser.
get_visible_pipelines	Get list of available pipeline names.

Snippet Management

Snippet	Handler for Python-based snippets.
snippets_modules_list	Load Python snippet modules.

Queue Management

QueueJob	Represents a job submitted to a queue.
SnippetRuntime	Helper class for building queue module implementations.

Profiles

Profile	Profile configuration container.
check_profile_files	Validate all file paths in profile.
check_programs_env_module	Verify environment modules in profile.

Utilities

Process Management

Command	High-level interface for executing commands with container support.
Namespace	Environment and dependency management system.
DockerConfig	Configuration for Docker and container runtime environments.
Volume	Volume binding configuration for containerized environments.

Error Handling

PypeError	Base exception for all pype errors.
PipelineError	Base class for pipeline-related errors.
SnippetError	Base class for snippet-related errors.
ProfileError	Base class for profile-related errors.
CommandError	Base class for command execution errors.