pipeline.nextflow

pipeline.nextflow

Run Nextflow workflows in local and HPC environments.

• init(output, pipeline_name=‘pipeline’, **kwargs) Initialize the launch directory by copying the system default config files.
• run(nextfile_path=None, nextflow_args=None, mode=“local”, pipeline_name=None, debug=False, hpc_options={}) Run a Nextflow workflow.

Functions

Name	Description
init	Initialize the launch directory by copying the system default config files
run	Run a Nextflow workflow

init

pipeline.nextflow.init(output, repo_base, pipeline_name='pipeline')

Initialize the launch directory by copying the system default config files

run

pipeline.nextflow.run(
    nextfile_path,
    mode='local',
    force_all=False,
    pipeline_name=None,
    nextflow_args=None,
    debug=False,
    hpc=get_hpc(),
)

Run a Nextflow workflow

Parameters

Name	Type	Description	Default
nextfile_path	str	Path to the Nextflow file.	required
nextflow_args	list	Additional Nextflow arguments. Defaults to an empty list.	None
mode	str	Execution mode. Defaults to “local”.	'local'

Raises

Name	Type	Description
	ValueError	If mode is ‘slurm’ but no HPC environment was detected.