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

Interface InputPreprocessor

All Known Implementing Classes:

CutAdaptInputPreprocessor, ExpressionInputPreprocessor, FastQCFixInputPreprocessor, FastQCInputPreprocessor, FeatureCountsInputPreprocessor, MapperInputPreprocessor, RnaSeqMetricsInputPreprocessor

public interface InputPreprocessor

This interface define a preprocessor for MultiQC input data.

Since:

2.2

Author:

Laurent Jourdren

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.

Method Details

getReportName

String getReportName()

Get the name of the report.

Returns:

the name of the report

getDataFormat

DataFormat getDataFormat()

Get the DataFormat handled by the preprocessor.

Returns:

the DataFormat handled by the preprocessor

preprocess

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

Preprocess data.

Parameters:

context - Step context

data - data to preprocess

multiQCInputDirectory - MultiQC input directory

Throws:

IOException - if an error occurs while preprocessing the data