module

biopipen.ns.splitpipe_pipeline

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The splitpipe pipeline

Parse Biosciences pipeline (split-pipe) processes plus a combine process to merge the sublibraries of a sequencing run and a summary process to summarize the metrics of multiple (combined) runs.

The reference genome is not built by this pipeline: build it once with the SplitPipeRef process and pass its output directory as genome_dir.

Classes
class

biopipen.ns.splitpipe_pipeline.SplitPipePipeline(*args, **kwds)

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Bases
pipen_args.procgroup.ProcGroup pipen.procgroup.ProcGroup

The splitpipe pipeline

Run split-pipe for the sublibraries of one sequencing run, combine them into a single dataset and summarize the metrics.

The reference genome must be built beforehand with the SplitPipeRef process (split-pipe --mode mkref), and its output directory passed as genome_dir.

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 the input and the genome</>
class

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

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Bases
abc.ABCMeta

Meta class for ProcGroup

Methods
  • __call__(cls, *args, **kwds) — Make sure Proc subclasses are singletons</>
staticmethod
__call__(cls, *args, **kwds)
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Make sure Proc subclasses are singletons

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

The Proc instance

classmethod

__init_subclass__()

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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)

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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)

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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 | pathlib.path | none, optional) — The output directory of the pipeline
  • **kwargs — The keyword arguments to pass to Pipen
Returns (Pipen)

The Pipen instance

method

post_init()

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Check the input and the genome