module

biopipen.ns.cnvkit_pipeline

</>

The CNVkit pipeline.

Classes
class

biopipen.ns.cnvkit_pipeline.CNVkitPipeline(*args, **kwds)

</>
Bases
pipen_args.procgroup.ProcGroup pipen.procgroup.ProcGroup

The CNVkit pipeline

Unlike cnvkit.py batch, this decouples the steps of the batch command so that we can control the details of each step.

Options for different processes can be specified by [CNVkitXXX.envs.xxx] See biopipen.ns.cnvkit.CNVkitXXX for more details.

To run this pipeline from command line, with the pipen-run plugin: 

>>> # In this case, `pipeline.cnvkit_pipeline.metafile` must be provided
>>> pipen run cnvkit_pipeline CNVkitPipeline <other pipeline args>

To use this as a dependency for other pipelines - 

>>> from biopipen.ns.cnvkit_pipeline import CNVkitPipeline
>>> pipeline = CNVkitPipeline(<options>)
>>> # pipeline.starts: Start processes of the pipeline
>>> # pipeline.ends: End processes of the pipeline
>>> # pipeline.procs.<proc>: The process with name <proc>

See also the docs for details https://pwwang.github.io/biopipen/pipelines/cnvkit_pipeline/

Attributes
  • parser — Pass arguments to initialize the parser
    The parser is a singleton and by default initalized at plugin.on_init() hook, which happens usually after the initialization of a process group. </>
Classes
Methods
  • __init_subclass__() — This method is called when a class is subclassed.</>
  • add_proc(self_or_method, proc) (Union) — Add a process to the proc group</>
  • as_pipen(name, desc, outdir, **kwargs) (Pipen) — Convert the pipeline to a Pipen instance</>
  • post_init() — Post initialization</>
class

pipen.procgroup.ProcGropuMeta(name, bases, namespace, **kwargs)

</>
Bases
abc.ABCMeta

Meta class for ProcGroup

Methods
staticmethod
register(cls, subclass)
</>

Register a virtual subclass of an ABC.

Returns the subclass, to allow usage as a class decorator.

staticmethod
__instancecheck__(cls, instance)
</>

Override for isinstance(instance, cls).

staticmethod
__subclasscheck__(cls, subclass)
</>

Override for issubclass(subclass, cls).

staticmethod
__call__(cls, *args, **kwds)
</>

Make sure Proc subclasses are singletons

Parameters
  • *args — and
  • **kwds — Arguments for the constructor
Returns

The Proc instance

classmethod

__init_subclass__()

</>

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

staticmethod

add_proc(self_or_method, proc=None)

</>

Add a process to the proc group

It works either as a decorator to the process directly or as a decorator to a method that returns the process.

Parameters
  • self_or_method (Union) — The proc group instance or a method thatreturns the process
  • proc (Optional, optional) — The process class if self_or_method is the proc group
Returns (Union)

The process class if self_or_method is the proc group, ora cached property that returns the process class

method

as_pipen(name=None, desc=None, outdir=None, **kwargs)

</>

Convert the pipeline to a Pipen instance

Parameters
  • name (str | none, optional) — The name of the pipeline
  • desc (str | none, optional) — The description of the pipeline
  • outdir (str | os.pathlike | none, optional) — The output directory of the pipeline
  • **kwargs — The keyword arguments to pass to Pipen
Returns (Pipen)

The Pipen instance

method

post_init()

</>

Post initialization

This method is called after arguments are parsed and set to self.opts This method is called before runtime processes are loaded