datalad.api.x_snakemake

datalad.api.x_snakemake(smargs=None, dataset=None)

Thin wrapper around SnakeMake to obtain file content prior processing

When snakemake is called through this wrapper, it is patched to use DataLad to ensure that file content is obtained prior access by snakemake. However, only content of files that are actually required for a particular workflow execution will be obtained.

Parameters
  • smargs -- Start with '--' before any snakemake argument to ensure such arguments are not processed by DataLad. [Default: None]

  • dataset (Dataset or None, optional) -- [Default: None]

  • on_failure ({'ignore', 'continue', 'stop'}, optional) -- behavior to perform on failure: 'ignore' any failure is reported, but does not cause an exception; 'continue' if any failure occurs an exception will be raised at the end, but processing other actions will continue for as long as possible; 'stop': processing will stop on first failure and an exception is raised. A failure is any result with status 'impossible' or 'error'. Raised exception is an IncompleteResultsError that carries the result dictionaries of the failures in its failed attribute. [Default: 'continue']

  • result_filter (callable or None, optional) -- if given, each to-be-returned status dictionary is passed to this callable, and is only returned if the callable's return value does not evaluate to False or a ValueError exception is raised. If the given callable supports **kwargs it will additionally be passed the keyword arguments of the original API call. [Default: None]

  • result_renderer ({'default', 'json', 'json_pp', 'tailored'} or None, optional) -- format of return value rendering on stdout. [Default: None]

  • result_xfm ({'datasets', 'successdatasets-or-none', 'paths', 'relpaths', 'metadata'} or callable or None, optional) -- if given, each to-be-returned result status dictionary is passed to this callable, and its return value becomes the result instead. This is different from result_filter, as it can perform arbitrary transformation of the result value. This is mostly useful for top- level command invocations that need to provide the results in a particular format. Instead of a callable, a label for a pre-crafted result transformation can be given. [Default: None]

  • return_type ({'generator', 'list', 'item-or-list'}, optional) -- return value behavior switch. If 'item-or-list' a single value is returned instead of a one-item return value list, or a list in case of multiple return values. None is return in case of an empty list. [Default: 'list']