module

biopipen.ns.cellranger_pipeline

</>

The cellranger pipelines

Primarily cellranger process plus summary for summarizing the metrics for multiple samples.

Classes
class

biopipen.ns.cellranger_pipeline.CellRangerCountPipeline(*args, **kwds)

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

The cellranger count pipeline

Run cellranger count for multiple samples and summarize the metrics.

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() — Check if the input is a list of fastq files</>
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()

</>

Check if the input is a list of fastq files

class

biopipen.ns.cellranger_pipeline.CellRangerVdjPipeline(*args, **kwds)

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

The cellranger vdj pipeline

Run cellranger vdj for multiple samples and summarize the metrics.

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() — Check if the input is a list of fastq files</>
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()

</>

Check if the input is a list of fastq files