camber.nextflow

The camber.nextflow handles workloads that uses the Nextflow framework and is deployed on Kubernetes as execution platform. It is a subclass of the CamberEngine that encapsulates the Python interface for Nextflow CLI.

Example

from camber import nextflow

nf_hello_job = nextflow.create_job(
    pipeline="nextflow-io/hello",
    engine_size="XSMALL",
    num_engines=4
)
# More nextflow workflow below

Methods

create_job

Creates a job to run a given pipeline using the NextflowEngine. Please note that if the pipeline requires the output directory, it should be placed in /camber_outputs. So when a job finishes, the output data will appear in the private stash jobs/<job_id>/outputs.

Args

pipeline: str

Supply a remote nextflow pipeline or a local one in the private stash. For remote pipelines, you can discover them more in nf-core pipelines.

engine_size: str

The size of the engine. One of XMICRO, MICRO, XXSMALL, XSMALL, SMALL, MEDIUM, or LARGE.

Default is XSMALL.

num_engines: Optional[int]

The number of engines will handle multiple tasks in a parallel manner.

Default is 1

params: Optional[Dict]

Define parameters for the pipeline. In case the pipeline requires passing input files to the params, the path of input files should be relative to the current working directory.

Example: {"--input": "./samplesheet.csv"}

Returns

CamberJob

An instance of the CamberJob class representing the created job.