pipeline.nextflow

pipeline.nextflow

Run Nextflow workflows in local and HPC environments.

• run(nextfile_path=None, nextflow_args=None, mode=“local”, pipeline_name=None, debug=False, hpc_options={}) Run a Nextflow workflow.

Functions

Name	Description
run	Run a Nextflow workflow

run

pipeline.nextflow.run(
    nextfile_path,
    nextflow_args=[],
    mode='local',
    pipeline_name=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.	[]
mode	str	Execution mode. Defaults to “local”.	'local'

Raises

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