Package fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Class IDRModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
All Implemented Interfaces:
Module
public class IDRModule extends AbstractModule
This class defines the IDR quality check step. This QC step determines the reproducibility of peaks between replicates.
Author:
Pierre-Marie Chiaroni - CSB lab - ENS - Paris, Celine Hernandez - CSB lab - ENS - Paris

  • Constructor Details

    • IDRModule

      public IDRModule()

  • Method Details

    • getName

      public String getName()
      Name of the Step.
      Returns:
      the name of the module

    • getDescription

      public String getDescription()
      A short description of the tool and what is done in the step.
      Specified by:
      getDescription in interface Module
      Overrides:
      getDescription in class AbstractModule
      Returns:
      the description of the module

    • getVersion

      public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
      Version.
      Returns:
      a Version object with the version of the Module

    • getInputPorts

      public InputPorts getInputPorts()
      Define input ports.
      Specified by:
      getInputPorts in interface Module
      Overrides:
      getInputPorts in class AbstractModule
      Returns:
      a set with DataFormat or null if the module does not any need input format

    • configure

      public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
      Set IDR parameters to configure the step. As written in IDR documentation, concerning parameter peak.half.width : "IMPORTANT: Currrently this parameter does not work properly so please pre-truncate your peaks if desired before feeding to IDR. Always set this parameter to -1."
      Specified by:
      configure in interface Module
      Overrides:
      configure in class AbstractModule
      Parameters:
      context - step configuration context
      stepParameters - parameters of the step
      Throws:
      EoulsanException - if a parameter is invalid

    • execute

      public TaskResult execute(TaskContext context, TaskStatus status)
      Install all the files necessary in the tmp folder, then run idr.
      Parameters:
      context - Execution context
      status - of the task
      Returns:
      a TaskResult object