module

biopipen.ns.cnv

</>

CNV/CNA-related processes, mostly tertiary analysis

Classes
class

biopipen.ns.cnv.AneuploidyScore(*args, **kwds) → Proc

</>
Bases
biopipen.core.proc.Proc pipen.proc.Proc

Chromosomal arm SCNA/aneuploidy

The CAAs in this process are calculated using Cohen-Sharir method See https://github.com/quevedor2/aneuploidy_score

Attributes
  • cache — Should we detect whether the jobs are cached?
  • desc — The description of the process. Will use the summary fromthe docstring by default.
  • dirsig — When checking the signature for caching, whether should we walkthrough the content of the directory? This is sometimes time-consuming if the directory is big.
  • envs — The arguments that are job-independent, useful for common optionsacross jobs.
  • envs_depth — How deep to update the envs when subclassed.
  • error_strategy — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • export — When True, the results will be exported to <pipeline.outdir>Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • forks — How many jobs to run simultaneously?
  • input — The keys for the input channel
  • input_data — The input data (will be computed for dependent processes)
  • lang — The language for the script to run. Should be the path to theinterpreter if lang is not in $PATH.
  • name — The name of the process. Will use the class name by default.
  • nexts — Computed from requires to build the process relationships
  • num_retries — How many times to retry to jobs once error occurs
  • order — The execution order for this process. The bigger the numberis, the later the process will be executed. Default: 0. Note that the dependent processes will always be executed first. This doesn't work for start processes either, whose orders are determined by Pipen.set_starts()
  • output — The output keys for the output channel(the data will be computed)
  • output_data — The output data (to pass to the next processes)
  • plugin_opts — Options for process-level plugins
  • requires — The dependency processes
  • scheduler — The scheduler to run the jobs
  • scheduler_opts — The options for the scheduler
  • script — The script template for the process
  • submission_batch — How many jobs to be submited simultaneously
  • template — Define the template engine to use.This could be either a template engine or a dict with key engine indicating the template engine and the rest the arguments passed to the constructor of the pipen.template.Template object. The template engine could be either the name of the engine, currently jinja2 and liquidpy are supported, or a subclass of pipen.template.Template. You can subclass pipen.template.Template to use your own template engine.
Input
  • segfile — The seg file, generally including chrom, start, end andseg.mean (the log2 ratio). It is typically a tab-delimited file or a BED file. If so, envs.chrom_col, envs.start_col, envs.end_col and envs.seg_col are the 1st, 2nd, 3rd and 5th columns, respectively. It can also be a VCF file. If so, envs.chrom_col and envs.start_col are not required. end_col and envs.seg_col will be a field in the INFO column. VariantAnnotation is required to extract the INFO field.
Output
  • outdir — The output directory containing the CAAs, AS and a histogramplot to show the CAAs for each chromosome arm
Envs
  • chrom_col — The column name for chromosome
  • cn_col — The column name for copy number
  • cn_transform (type=auto) — A R function to transform seg.mean intocopy number, or a list of cutoffs to determine the copy number. See https://cnvkit.readthedocs.io/en/stable/pipeline.html#calling-methods. If this is give, cn_col will be ignored.
  • end_col — The column name for end position
  • excl_chroms (list) — The chromosomes to be excludedWorks with/without chr prefix.
  • genome — The genome version, hg19 or hg38
  • seg_col — The column name for seg.mean
  • segmean_transform (text) — A R function to transform seg.meanThe transformed value will be used to calculate the CAAs
  • start_col — The column name for start position
  • threshold (type=float) — The threshold to determine whether a chromosomearm is gained or lost.
  • wgd_gf (type=float) — The fraction of the genome that is affected by WGD
Requires
  • AneuploidyScore —
    • check: {{proc.lang}} <(echo "library(AneuploidyScore)")
  • ucsc.hg19.cytoband —
    • if: {{ proc.envs.genome == 'hg19' }}
    • check: {{proc.lang}} <(echo "library(ucsc.hg19.cytoband)")
  • ucsc.hg38.cytoband —
    • if: {{ proc.envs.genome == 'hg38' }}
    • check: {{proc.lang}} <(echo "library(ucsc.hg38.cytoband)")
Classes
Methods
  • __init_subclass__() — Do the requirements inferring since we need them to build up theprocess relationship </>
  • from_proc(proc, name, desc, envs, envs_depth, cache, export, error_strategy, num_retries, forks, input_data, order, plugin_opts, requires, scheduler, scheduler_opts, submission_batch) (Type) — Create a subclass of Proc using another Proc subclass or Proc itself</>
  • gc() — GC process for the process to save memory after it's done</>
  • init() — Init all other properties and jobs</>
  • log(level, msg, *args, logger) — Log message for the process</>
  • run() — Run the process</>
class

pipen.proc.ProcMeta(name, bases, namespace, **kwargs)

</>
Bases
abc.ABCMeta

Meta class for Proc

Methods
  • __call__(cls, *args, **kwds) (Proc) — Make sure Proc subclasses are singletons</>
  • __instancecheck__(cls, instance) — Override for isinstance(instance, cls).</>
  • __repr__(cls) (str) — Representation for the Proc subclasses</>
  • __subclasscheck__(cls, subclass) — Override for issubclass(subclass, cls).</>
  • register(cls, subclass) — Register a virtual subclass of an ABC.</>
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
__repr__(cls) → str
</>

Representation for the Proc subclasses

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

Make sure Proc subclasses are singletons

Parameters
  • *args (Any) — and
  • **kwds (Any) — Arguments for the constructor
Returns (Proc)

The Proc instance

classmethod

from_proc(proc, name=None, desc=None, envs=None, envs_depth=None, cache=None, export=None, error_strategy=None, num_retries=None, forks=None, input_data=None, order=None, plugin_opts=None, requires=None, scheduler=None, scheduler_opts=None, submission_batch=None)

</>

Create a subclass of Proc using another Proc subclass or Proc itself

Parameters
  • proc (Type) — The Proc subclass
  • name (str, optional) — The new name of the process
  • desc (str, optional) — The new description of the process
  • envs (Mapping, optional) — The arguments of the process, will overwrite parent oneThe items that are specified will be inherited
  • envs_depth (int, optional) — How deep to update the envs when subclassed.
  • cache (bool, optional) — Whether we should check the cache for the jobs
  • export (bool, optional) — When True, the results will be exported to<pipeline.outdir> Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • error_strategy (str, optional) — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • num_retries (int, optional) — How many times to retry to jobs once error occurs
  • forks (int, optional) — New forks for the new process
  • input_data (Any, optional) — The input data for the process. Only when this processis a start process
  • order (int, optional) — The order to execute the new process
  • plugin_opts (Mapping, optional) — The new plugin options, unspecified items will beinherited.
  • requires (Sequence, optional) — The required processes for the new process
  • scheduler (str, optional) — The new shedular to run the new process
  • scheduler_opts (Mapping, optional) — The new scheduler options, unspecified items willbe inherited.
  • submission_batch (int, optional) — How many jobs to be submited simultaneously
Returns (Type)

The new process class

classmethod

__init_subclass__()

</>

Do the requirements inferring since we need them to build up theprocess relationship

method

init()

</>

Init all other properties and jobs

method

gc()

</>

GC process for the process to save memory after it's done

method

log(level, msg, *args, logger=<LoggerAdapter pipen.core (WARNING)>)

</>

Log message for the process

Parameters
  • level (int | str) — The log level of the record
  • msg (str) — The message to log
  • *args — The arguments to format the message
  • logger (LoggerAdapter, optional) — The logging logger
method

run()

</>

Run the process

class

biopipen.ns.cnv.AneuploidyScoreSummary(*args, **kwds) → Proc

</>
Bases
biopipen.core.proc.Proc pipen.proc.Proc

Summary table and plots from AneuploidyScore

Attributes
  • cache — Should we detect whether the jobs are cached?
  • desc — The description of the process. Will use the summary fromthe docstring by default.
  • dirsig — When checking the signature for caching, whether should we walkthrough the content of the directory? This is sometimes time-consuming if the directory is big.
  • envs — The arguments that are job-independent, useful for common optionsacross jobs.
  • envs_depth — How deep to update the envs when subclassed.
  • error_strategy — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • export — When True, the results will be exported to <pipeline.outdir>Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • forks — How many jobs to run simultaneously?
  • input — The keys for the input channel
  • input_data — The input data (will be computed for dependent processes)
  • lang — The language for the script to run. Should be the path to theinterpreter if lang is not in $PATH.
  • name — The name of the process. Will use the class name by default.
  • nexts — Computed from requires to build the process relationships
  • num_retries — How many times to retry to jobs once error occurs
  • order — The execution order for this process. The bigger the numberis, the later the process will be executed. Default: 0. Note that the dependent processes will always be executed first. This doesn't work for start processes either, whose orders are determined by Pipen.set_starts()
  • output — The output keys for the output channel(the data will be computed)
  • output_data — The output data (to pass to the next processes)
  • plugin_opts — Options for process-level plugins
  • requires — The dependency processes
  • scheduler — The scheduler to run the jobs
  • scheduler_opts — The options for the scheduler
  • script — The script template for the process
  • submission_batch — How many jobs to be submited simultaneously
  • template — Define the template engine to use.This could be either a template engine or a dict with key engine indicating the template engine and the rest the arguments passed to the constructor of the pipen.template.Template object. The template engine could be either the name of the engine, currently jinja2 and liquidpy are supported, or a subclass of pipen.template.Template. You can subclass pipen.template.Template to use your own template engine.
Input
  • asdirs — The output directories from AneuploidyScore
  • metafile — The metafile containing the sample information
Output
  • outdir — The output directory containing the summary table and plots
Envs
  • group_cols (type=auto) — The column name in the metafile to group thesamples. We also support multiple columns, e.g. ["group1", "group2"] You can also use group1,group2 to add a secondary grouping based on group2 within each group1 (only works for 2 groups)
  • heatmap_cases (type=json) — The cases to be included in the heatmapBy default, all arms are included. If specified, keys are the names of the cases and values are the arms, which will be included in the heatmap. The list of arms should be a subset of chr<N>_p and chr<N>_q, where <N> is the chromosome number from 1 to 22, X, Y. You can also use ALL to include all arms.
  • sample_name (text) — An R function to extract the sample name fromthe file stem (not including .aneuploidy_score part)
Classes
Methods
  • __init_subclass__() — Do the requirements inferring since we need them to build up theprocess relationship </>
  • from_proc(proc, name, desc, envs, envs_depth, cache, export, error_strategy, num_retries, forks, input_data, order, plugin_opts, requires, scheduler, scheduler_opts, submission_batch) (Type) — Create a subclass of Proc using another Proc subclass or Proc itself</>
  • gc() — GC process for the process to save memory after it's done</>
  • init() — Init all other properties and jobs</>
  • log(level, msg, *args, logger) — Log message for the process</>
  • run() — Run the process</>
class

pipen.proc.ProcMeta(name, bases, namespace, **kwargs)

</>
Bases
abc.ABCMeta

Meta class for Proc

Methods
  • __call__(cls, *args, **kwds) (Proc) — Make sure Proc subclasses are singletons</>
  • __instancecheck__(cls, instance) — Override for isinstance(instance, cls).</>
  • __repr__(cls) (str) — Representation for the Proc subclasses</>
  • __subclasscheck__(cls, subclass) — Override for issubclass(subclass, cls).</>
  • register(cls, subclass) — Register a virtual subclass of an ABC.</>
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
__repr__(cls) → str
</>

Representation for the Proc subclasses

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

Make sure Proc subclasses are singletons

Parameters
  • *args (Any) — and
  • **kwds (Any) — Arguments for the constructor
Returns (Proc)

The Proc instance

classmethod

from_proc(proc, name=None, desc=None, envs=None, envs_depth=None, cache=None, export=None, error_strategy=None, num_retries=None, forks=None, input_data=None, order=None, plugin_opts=None, requires=None, scheduler=None, scheduler_opts=None, submission_batch=None)

</>

Create a subclass of Proc using another Proc subclass or Proc itself

Parameters
  • proc (Type) — The Proc subclass
  • name (str, optional) — The new name of the process
  • desc (str, optional) — The new description of the process
  • envs (Mapping, optional) — The arguments of the process, will overwrite parent oneThe items that are specified will be inherited
  • envs_depth (int, optional) — How deep to update the envs when subclassed.
  • cache (bool, optional) — Whether we should check the cache for the jobs
  • export (bool, optional) — When True, the results will be exported to<pipeline.outdir> Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • error_strategy (str, optional) — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • num_retries (int, optional) — How many times to retry to jobs once error occurs
  • forks (int, optional) — New forks for the new process
  • input_data (Any, optional) — The input data for the process. Only when this processis a start process
  • order (int, optional) — The order to execute the new process
  • plugin_opts (Mapping, optional) — The new plugin options, unspecified items will beinherited.
  • requires (Sequence, optional) — The required processes for the new process
  • scheduler (str, optional) — The new shedular to run the new process
  • scheduler_opts (Mapping, optional) — The new scheduler options, unspecified items willbe inherited.
  • submission_batch (int, optional) — How many jobs to be submited simultaneously
Returns (Type)

The new process class

classmethod

__init_subclass__()

</>

Do the requirements inferring since we need them to build up theprocess relationship

method

init()

</>

Init all other properties and jobs

method

gc()

</>

GC process for the process to save memory after it's done

method

log(level, msg, *args, logger=<LoggerAdapter pipen.core (WARNING)>)

</>

Log message for the process

Parameters
  • level (int | str) — The log level of the record
  • msg (str) — The message to log
  • *args — The arguments to format the message
  • logger (LoggerAdapter, optional) — The logging logger
method

run()

</>

Run the process

class

biopipen.ns.cnv.TMADScore(*args, **kwds) → Proc

</>
Bases
biopipen.core.proc.Proc pipen.proc.Proc

Trimmed Median Absolute Deviation (TMAD) score for CNV

Reference: Mouliere, Chandrananda, Piskorz and Moore et al. Enhanced detection of circulating tumor DNA by fragment size analysis Science Translational Medicine (2018).

Attributes
  • cache — Should we detect whether the jobs are cached?
  • desc — The description of the process. Will use the summary fromthe docstring by default.
  • dirsig — When checking the signature for caching, whether should we walkthrough the content of the directory? This is sometimes time-consuming if the directory is big.
  • envs — The arguments that are job-independent, useful for common optionsacross jobs.
  • envs_depth — How deep to update the envs when subclassed.
  • error_strategy — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • export — When True, the results will be exported to <pipeline.outdir>Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • forks — How many jobs to run simultaneously?
  • input — The keys for the input channel
  • input_data — The input data (will be computed for dependent processes)
  • lang — The language for the script to run. Should be the path to theinterpreter if lang is not in $PATH.
  • name — The name of the process. Will use the class name by default.
  • nexts — Computed from requires to build the process relationships
  • num_retries — How many times to retry to jobs once error occurs
  • order — The execution order for this process. The bigger the numberis, the later the process will be executed. Default: 0. Note that the dependent processes will always be executed first. This doesn't work for start processes either, whose orders are determined by Pipen.set_starts()
  • output — The output keys for the output channel(the data will be computed)
  • output_data — The output data (to pass to the next processes)
  • plugin_opts — Options for process-level plugins
  • requires — The dependency processes
  • scheduler — The scheduler to run the jobs
  • scheduler_opts — The options for the scheduler
  • script — The script template for the process
  • submission_batch — How many jobs to be submited simultaneously
  • template — Define the template engine to use.This could be either a template engine or a dict with key engine indicating the template engine and the rest the arguments passed to the constructor of the pipen.template.Template object. The template engine could be either the name of the engine, currently jinja2 and liquidpy are supported, or a subclass of pipen.template.Template. You can subclass pipen.template.Template to use your own template engine.
Input
  • segfile — The seg file, two columns are required:
    • * chrom: The chromosome name, used for filtering
    • * seg.mean: The log2 ratio.
    It is typically a tab-delimited file or a BED file.If so, envs.chrom_col and envs.seg_col are the 1st and 5th columns, respectively. It can also be a VCF file. If so, envs.chrom_col and envs.start_col are not required. end_col and envs.seg_col will be a field in the INFO column. VariantAnnotation is required to extract the INFO field.
Output
  • outfile — The output file containing the TMAD score
Envs
  • chrom_col — The column name for chromosome
  • excl_chroms (list) — The chromosomes to be excluded
  • seg_col — The column name for seg.mean
  • segmean_transform — The transformation function for seg.mean
Classes
Methods
  • __init_subclass__() — Do the requirements inferring since we need them to build up theprocess relationship </>
  • from_proc(proc, name, desc, envs, envs_depth, cache, export, error_strategy, num_retries, forks, input_data, order, plugin_opts, requires, scheduler, scheduler_opts, submission_batch) (Type) — Create a subclass of Proc using another Proc subclass or Proc itself</>
  • gc() — GC process for the process to save memory after it's done</>
  • init() — Init all other properties and jobs</>
  • log(level, msg, *args, logger) — Log message for the process</>
  • run() — Run the process</>
class

pipen.proc.ProcMeta(name, bases, namespace, **kwargs)

</>
Bases
abc.ABCMeta

Meta class for Proc

Methods
  • __call__(cls, *args, **kwds) (Proc) — Make sure Proc subclasses are singletons</>
  • __instancecheck__(cls, instance) — Override for isinstance(instance, cls).</>
  • __repr__(cls) (str) — Representation for the Proc subclasses</>
  • __subclasscheck__(cls, subclass) — Override for issubclass(subclass, cls).</>
  • register(cls, subclass) — Register a virtual subclass of an ABC.</>
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
__repr__(cls) → str
</>

Representation for the Proc subclasses

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

Make sure Proc subclasses are singletons

Parameters
  • *args (Any) — and
  • **kwds (Any) — Arguments for the constructor
Returns (Proc)

The Proc instance

classmethod

from_proc(proc, name=None, desc=None, envs=None, envs_depth=None, cache=None, export=None, error_strategy=None, num_retries=None, forks=None, input_data=None, order=None, plugin_opts=None, requires=None, scheduler=None, scheduler_opts=None, submission_batch=None)

</>

Create a subclass of Proc using another Proc subclass or Proc itself

Parameters
  • proc (Type) — The Proc subclass
  • name (str, optional) — The new name of the process
  • desc (str, optional) — The new description of the process
  • envs (Mapping, optional) — The arguments of the process, will overwrite parent oneThe items that are specified will be inherited
  • envs_depth (int, optional) — How deep to update the envs when subclassed.
  • cache (bool, optional) — Whether we should check the cache for the jobs
  • export (bool, optional) — When True, the results will be exported to<pipeline.outdir> Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • error_strategy (str, optional) — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • num_retries (int, optional) — How many times to retry to jobs once error occurs
  • forks (int, optional) — New forks for the new process
  • input_data (Any, optional) — The input data for the process. Only when this processis a start process
  • order (int, optional) — The order to execute the new process
  • plugin_opts (Mapping, optional) — The new plugin options, unspecified items will beinherited.
  • requires (Sequence, optional) — The required processes for the new process
  • scheduler (str, optional) — The new shedular to run the new process
  • scheduler_opts (Mapping, optional) — The new scheduler options, unspecified items willbe inherited.
  • submission_batch (int, optional) — How many jobs to be submited simultaneously
Returns (Type)

The new process class

classmethod

__init_subclass__()

</>

Do the requirements inferring since we need them to build up theprocess relationship

method

init()

</>

Init all other properties and jobs

method

gc()

</>

GC process for the process to save memory after it's done

method

log(level, msg, *args, logger=<LoggerAdapter pipen.core (WARNING)>)

</>

Log message for the process

Parameters
  • level (int | str) — The log level of the record
  • msg (str) — The message to log
  • *args — The arguments to format the message
  • logger (LoggerAdapter, optional) — The logging logger
method

run()

</>

Run the process

class

biopipen.ns.cnv.TMADScoreSummary(*args, **kwds) → Proc

</>
Bases
biopipen.core.proc.Proc pipen.proc.Proc

Summary table and plots for TMADScore

Attributes
  • cache — Should we detect whether the jobs are cached?
  • desc — The description of the process. Will use the summary fromthe docstring by default.
  • dirsig — When checking the signature for caching, whether should we walkthrough the content of the directory? This is sometimes time-consuming if the directory is big.
  • envs — The arguments that are job-independent, useful for common optionsacross jobs.
  • envs_depth — How deep to update the envs when subclassed.
  • error_strategy — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • export — When True, the results will be exported to <pipeline.outdir>Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • forks — How many jobs to run simultaneously?
  • input — The keys for the input channel
  • input_data — The input data (will be computed for dependent processes)
  • lang — The language for the script to run. Should be the path to theinterpreter if lang is not in $PATH.
  • name — The name of the process. Will use the class name by default.
  • nexts — Computed from requires to build the process relationships
  • num_retries — How many times to retry to jobs once error occurs
  • order — The execution order for this process. The bigger the numberis, the later the process will be executed. Default: 0. Note that the dependent processes will always be executed first. This doesn't work for start processes either, whose orders are determined by Pipen.set_starts()
  • output — The output keys for the output channel(the data will be computed)
  • output_data — The output data (to pass to the next processes)
  • plugin_opts — Options for process-level plugins
  • requires — The dependency processes
  • scheduler — The scheduler to run the jobs
  • scheduler_opts — The options for the scheduler
  • script — The script template for the process
  • submission_batch — How many jobs to be submited simultaneously
  • template — Define the template engine to use.This could be either a template engine or a dict with key engine indicating the template engine and the rest the arguments passed to the constructor of the pipen.template.Template object. The template engine could be either the name of the engine, currently jinja2 and liquidpy are supported, or a subclass of pipen.template.Template. You can subclass pipen.template.Template to use your own template engine.
Input
  • metafile — The metafile containing the sample informationThe first column must be the sample ID
  • tmadfiles — The output files from TMADScore
Output
  • outdir — The output directory containing the summary table and plots
Envs
  • group_cols (type=auto) — The column name in the metafile to group thesamples Could also be a list of column names If not specified, samples will be plotted individually as a barplot We also support multiple columns, e.g. ["group1", "group2"] You can also use group1,group2 to add a secondary grouping based on group2 within each group1 (only works for 2 groups)
  • sample_name (text) — An R function to extract the sample name fromthe file stem (not including .tmad.txt part)
Classes
Methods
  • __init_subclass__() — Do the requirements inferring since we need them to build up theprocess relationship </>
  • from_proc(proc, name, desc, envs, envs_depth, cache, export, error_strategy, num_retries, forks, input_data, order, plugin_opts, requires, scheduler, scheduler_opts, submission_batch) (Type) — Create a subclass of Proc using another Proc subclass or Proc itself</>
  • gc() — GC process for the process to save memory after it's done</>
  • init() — Init all other properties and jobs</>
  • log(level, msg, *args, logger) — Log message for the process</>
  • run() — Run the process</>
class

pipen.proc.ProcMeta(name, bases, namespace, **kwargs)

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Bases
abc.ABCMeta

Meta class for Proc

Methods
  • __call__(cls, *args, **kwds) (Proc) — Make sure Proc subclasses are singletons</>
  • __instancecheck__(cls, instance) — Override for isinstance(instance, cls).</>
  • __repr__(cls) (str) — Representation for the Proc subclasses</>
  • __subclasscheck__(cls, subclass) — Override for issubclass(subclass, cls).</>
  • register(cls, subclass) — Register a virtual subclass of an ABC.</>
staticmethod
register(cls, subclass)
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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)
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Override for issubclass(subclass, cls).

staticmethod
__repr__(cls) → str
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Representation for the Proc subclasses

staticmethod
__call__(cls, *args, **kwds)
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Make sure Proc subclasses are singletons

Parameters
  • *args (Any) — and
  • **kwds (Any) — Arguments for the constructor
Returns (Proc)

The Proc instance

classmethod

from_proc(proc, name=None, desc=None, envs=None, envs_depth=None, cache=None, export=None, error_strategy=None, num_retries=None, forks=None, input_data=None, order=None, plugin_opts=None, requires=None, scheduler=None, scheduler_opts=None, submission_batch=None)

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Create a subclass of Proc using another Proc subclass or Proc itself

Parameters
  • proc (Type) — The Proc subclass
  • name (str, optional) — The new name of the process
  • desc (str, optional) — The new description of the process
  • envs (Mapping, optional) — The arguments of the process, will overwrite parent oneThe items that are specified will be inherited
  • envs_depth (int, optional) — How deep to update the envs when subclassed.
  • cache (bool, optional) — Whether we should check the cache for the jobs
  • export (bool, optional) — When True, the results will be exported to<pipeline.outdir> Defaults to None, meaning only end processes will export. You can set it to True/False to enable or disable exporting for processes
  • error_strategy (str, optional) — How to deal with the errors
    • - retry, ignore, halt
    • - halt to halt the whole pipeline, no submitting new jobs
    • - terminate to just terminate the job itself
  • num_retries (int, optional) — How many times to retry to jobs once error occurs
  • forks (int, optional) — New forks for the new process
  • input_data (Any, optional) — The input data for the process. Only when this processis a start process
  • order (int, optional) — The order to execute the new process
  • plugin_opts (Mapping, optional) — The new plugin options, unspecified items will beinherited.
  • requires (Sequence, optional) — The required processes for the new process
  • scheduler (str, optional) — The new shedular to run the new process
  • scheduler_opts (Mapping, optional) — The new scheduler options, unspecified items willbe inherited.
  • submission_batch (int, optional) — How many jobs to be submited simultaneously
Returns (Type)

The new process class

classmethod

__init_subclass__()

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Do the requirements inferring since we need them to build up theprocess relationship

method

init()

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Init all other properties and jobs

method

gc()

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GC process for the process to save memory after it's done

method

log(level, msg, *args, logger=<LoggerAdapter pipen.core (WARNING)>)

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Log message for the process

Parameters
  • level (int | str) — The log level of the record
  • msg (str) — The message to log
  • *args — The arguments to format the message
  • logger (LoggerAdapter, optional) — The logging logger
method

run()

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Run the process