Package fr.ens.biologie.genomique.eoulsan.modules.fastqc

Class FastQCModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
All Implemented Interfaces:
Module
public class FastQCModule extends AbstractModule
This class define a module that compute QC report using FastQC.
Since:
2.0
Author:
Sandrine Perrin

  • Field Details

    • FASTQC_KMER_SIZE_PARAMETER_NAME

      public static final String FASTQC_KMER_SIZE_PARAMETER_NAME
      Collector FastQC kmer size
      See Also:

    • FASTQC_NOGROUP_PARAMETER_NAME

      public static final String FASTQC_NOGROUP_PARAMETER_NAME
      Collector FastQC nogroup
      See Also:

    • FASTQC_EXPGROUP_PARAMETER_NAME

      public static final String FASTQC_EXPGROUP_PARAMETER_NAME
      Use exponential base groups in graph
      See Also:

    • FASTQC_CASAVA_PARAMETER_NAME

      public static final String FASTQC_CASAVA_PARAMETER_NAME
      Format fastq type casava/Illumina
      See Also:

    • FASTQC_NOFILTER_PARAMETER_NAME

      public static final String FASTQC_NOFILTER_PARAMETER_NAME
      Option for filter fastq file if casava=true for all modules
      See Also:

  • Constructor Details

    • FastQCModule

      public FastQCModule()

  • Method Details

    • getName

      public String getName()
      Description copied from interface: Module
      Get the name of the module.
      Returns:
      the name of the module

    • getDescription

      public String getDescription()
      Description copied from interface: Module
      Get the description of the module
      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()
      Description copied from interface: Module
      Get version of the Module.
      Returns:
      a Version object with the version of the Module

    • getInputPorts

      public InputPorts getInputPorts()
      Description copied from interface: Module
      Get the input data format.
      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

    • getOutputPorts

      public OutputPorts getOutputPorts()
      Description copied from interface: Module
      Get the output data format.
      Specified by:
      getOutputPorts in interface Module
      Overrides:
      getOutputPorts in class AbstractModule
      Returns:
      an set with DataFormat or null if the module does not produce any output data

    • configure

      public void configure(StepConfigurationContext context, Set<Parameter> stepParameters) throws EoulsanException
      Description copied from interface: Module
      Set the parameters of the step to configure the module.
      Specified by:
      configure in interface Module
      Overrides:
      configure in class AbstractModule
      Parameters:
      context - configuration context. The context can be null for generator steps
      stepParameters - parameters of the step
      Throws:
      EoulsanException - if a parameter is invalid

    • execute

      public TaskResult execute(TaskContext context, TaskStatus status)
      Description copied from interface: Module
      Execute a task step.
      Parameters:
      context - Execution context
      status - of the task
      Returns:
      a TaskResult object