Skip to main content

This package provides a stable interface for interactions between Snakemake and its executor plugins.

Project description

Stable interfaces and functionality for Snakemake executor plugins

This package provides a stable interface for interactions between Snakemake and its executor plugins (WIP).

Plugins should implement the following skeleton to comply with this interface:

from snakemake_interface_executor_plugins.executors.remote import RemoteExecutor
from snakemake_interface_executor_plugins import ExecutorSettingsBase, CommonSettings

# Optional:
# define additional settings for your executor
# They will occur in the Snakemake CLI as --<executor-name>-<param-name>
# Omit this class if you don't need any.
@dataclass
class ExecutorSettings:
    myparam: int=field(default=None, metadata={"help": "Some help text"})


# Specify common settings shared by various executors.
common_settings = CommonSettings(
    # define whether your executor plugin executes locally
    # or remotely. In virtually all cases, it will be remote execution
    # (cluster, cloud, etc.). Only Snakemake's standard execution 
    # plugins (snakemake-executor-plugin-dryrun, snakemake-executor-plugin-local)
    # are expected to specify False here.
    non_local_exec=True
)


# Required:
# Implementation of your executor
class Executor(RemoteExecutor)
    def __init__(
        self,
        workflow: WorkflowExecutorInterface,
        dag: DAGExecutorInterface,
        stats: StatsExecutorInterface,
        logger: LoggerExecutorInterface,
        executor_settings: Optional[ExecutorSettings], # if no ExecutorSettings are defined above, this will receive None
    ):
    super().__init__(
        workflow,
        dag,
        stats,
        logger,
        executor_settings,
        # configure behavior of RemoteExecutor below
        max_status_checks_per_second=1, # how many status checks should be performed per second
        disable_default_remote_provider_args=False, # whether arguments for setting the remote provider shall not be passed to jobs
        disable_default_resources_args=False, # whether arguments for setting default resources shall not be passed to jobs
        disable_envvar_declarations=False, # whether environment variables shall not be passed to jobs
    )
    # access executor specific settings 
    self.executor_settings
    # access workflow
    self.workflow

    # IMPORTANT: in your plugin, only access methods and properties of Snakemake objects (like Workflow, Persistence, etc.)
    # that are defined in the interfaces found in THIS package. Other parts of those objects
    # are NOT guaranteed to remain the same across new releases.

    # To ensure that the used interfaces are not changing, you should depend on this package as
    # >=a.b.c,<d with d=a+1 (i.e. pin the dependency on this package to be at least the version at time of development
    # and less than the next major version which would introduce breaking changes).

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

Built Distribution

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page