auto_process_ngs.qc.modules

class auto_process_ngs.qc.modules.QCDir(qc_dir, fastq_attrs=None)

Helper class for interacting with a QC directory

Provides the following attributes/properties:

  • path: full path to the QC directory

  • fastq_attrs: class for extracting information from Fastq filenames

  • info: AnalysisProjectQCDirInfo instance loaded with metadata from ‘qc.info’ (or None if there is no info file)

  • file_list: list of paths for files and directories under the the QC directory

Parameters:

  • qc_dir (str) – path to the QC dir

  • fastq_attrs (object) – optional class for extracting info from Fastq filenames (default: AnalysisFastq)

property file_list

Returns list of file and directory paths under QC dir

The list contains the full path for each file and directory.

class auto_process_ngs.qc.modules.QCModule

Base class for defining and handling QC modules

add_to_pipeline(p, *args, **kws)

Add the QC module tasks to a pipeline

Should be implemented by the subclass to add the tasks required to execute the QC module to an existing pipeline, and return the final task instance.

Parameters:

  • p (Pipeline) – pipeline instance

  • args (list) – positional arguments required by the QC module

  • kws (mapping) – additional optional arguments for configuring the module

classmethod collect_qc_outputs(qc_dir)

Collect information on QC module outputs

Should be implemented by the subclass to handle the specific outputs from the QC module, and return an AttributeDictionary with the collected data.

Parameters:

qc_dir (QCDir) – QC directory to examine

classmethod verify(params, qc_outputs)

Verify the outputs of the QC module

Should be implemented by the subclass to perform the verification based on the supplied parameters and the collected outputs.

Should return one of 3 values:

  • True: outputs verified ok

  • False: outputs failed to verify

  • None: verification not possible

Parameters:

  • params (AttributeDictionary) – values of parameters used as inputs to the QC module

  • qc_outputs (AttributeDictionary) – QC outputs returned from the ‘collect_qc_outputs’ method