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

Class FastQCInputPreprocessor

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor

All Implemented Interfaces:

InputPreprocessor

Direct Known Subclasses:

FastQCFixInputPreprocessor

public class FastQCInputPreprocessor
extends Object
implements InputPreprocessor

This class define a preprocessor for FastQC reports.

Since:

2.2

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static final String	REPORT_NAME

Constructor Summary

Constructors

Constructor	Description
FastQCInputPreprocessor()

Method Summary

Modifier and Type	Method	Description
DataFormat	getDataFormat()	Get the DataFormat handled by the preprocessor.
String	getReportName()	Get the name of the report.
void	preprocess(TaskContext context, Data data, File multiQCInputDirectory)	Preprocess data.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

REPORT_NAME

public static final String REPORT_NAME

See Also:

• Constant Field Values

Constructor Details

FastQCInputPreprocessor

public FastQCInputPreprocessor()

Method Details

getReportName

public String getReportName()

Description copied from interface: InputPreprocessor

Get the name of the report.

Specified by:

getReportName in interface InputPreprocessor

Returns:

the name of the report

getDataFormat

public DataFormat getDataFormat()

Description copied from interface: InputPreprocessor

Get the DataFormat handled by the preprocessor.

Specified by:

getDataFormat in interface InputPreprocessor

Returns:

the DataFormat handled by the preprocessor

preprocess

public void preprocess(TaskContext context,
 Data data,
 File multiQCInputDirectory)
                throws IOException

Description copied from interface: InputPreprocessor

Preprocess data.

Specified by:

preprocess in interface InputPreprocessor

Parameters:

context - Step context

data - data to preprocess

multiQCInputDirectory - MultiQC input directory

Throws:

IOException - if an error occurs while preprocessing the data