Skip to content

module snakemake.run

Module for executing Snakemake workflows.

Global Variables

  • DUMMY_DATA

class SnakemakeExecutor

Run snakemake with system calls.

Args:

  • run_config: Run-specific parameters.
  • exec_dir: Directory in which the run is executed.
  • config_file: Path to Snakemake configuration file.
  • bind_paths: Paths to bind to Singularity container.

Attributes:

  • run_config: Run-specific parameters.
  • exec_dir: Directory in which the run is executed.
  • config_file: Path to Snakemake configuration file.
  • bind_paths: Paths to bind to Singularity container.
  • run_state: State of the run.

method __init__

__init__(
    run_config: ConfigRun,
    exec_dir: Path = PosixPath('/home/runner/work/zarp-cli/zarp-cli'),
    config_file: Optional[Path] = None,
    bind_paths: Optional[List[Path]] = None
) → None

Class constructor.

method compile_command

compile_command(snakefile: Path) → List[str]

Compile Snakemake command as list of strings.

Args:

  • snakefile: Path to Snakemake descriptor file.

method run

run(cmd) → None

Run Snakemake command.

Run Snakemake workflow with a system call. The run state is set to SUCCESS if the run was successful, and to ERROR if the run failed.

Args:

  • cmd: Snakemake command as list of strings.

Raises:

  • CalledProcessError: If the Snakemake run failed.