package

biopipen.core

</>
module

biopipen.core.filters

</>

Additional filters for pipen

Functions
  • dict_to_cli_args(dic, exclude, prefix, sep, dup_key, join, start_key, end_key, dashify) (Union) — Convert a python dict to a string of CLI arguments</>
  • r(obj, ignoreintkey, todot, sortkeys, skip, _i) (str) — Convert a python object into R repr</>
  • source_r(path) (str) — Source an R script.</>
module

biopipen.core.defaults

</>

Provide default variables

  • BIOPIPEN_DIR: the root directory of the biopipen source
  • REPORT_DIR: the root directory of the report
  • SCRIPTS_DIR: the root directory of the scripts
module

biopipen.core.testing

</>

Provide utilities for testing.

Functions
  • get_pipeline(testfile, loglevel, enable_report, **kwargs) — Get a pipeline for a test file</>
  • r_test(mem) (callable) — A decorator to test R code</>
module

biopipen.core.config

</>

Provides the envs from configuration files

Classes
  • ConfigItems — Provides the envs from configuration files and defaults thenon-existing values to None. </>
module

biopipen.core.proc

</>

Provides a base class for the processes to subclass

Classes
  • Proc (Proc) — Base class for all processes in biopipen to subclass</>