net.sourceforge.seqware.pipeline.module (SeqWare 1.1.2 API)

Interface Summary
Interface	Description
ModuleInterface	This interface defines the required behavior of a SeqWare module.
RedirectAware	This module, in conjunction with the Tag and Run annotation are used to replace the old Module with the Runner code.

Class Summary
Class Description

Module
Abstract Module class.

TestModule
This is an empty module mainly for testing purpose.
Enum Summary
Enum Description

ModuleMethod
Enumeration class for ModuleMethod Created by IntelliJ IDEA.

Class Summary
Class	Description
Module	Abstract Module class.
TestModule	This is an empty module mainly for testing purpose.

Enum Summary
Enum	Description
ModuleMethod	Enumeration class for ModuleMethod Created by IntelliJ IDEA.

Annotation Types Summary
Annotation Type	Description
StderrRedirect	Annotation type to tag where to start Stderr redirect Created by IntelliJ IDEA.
StdoutRedirect	Interface for declaring when to do the Created by IntelliJ IDEA.

Package net.sourceforge.seqware.pipeline.module Description

This package provides the SeqWare module interface and API, including common code and classes. SeqWare uses modules as the main unit oF processing. Most modules will wrap a command-line tool providing a uniform way to call it and capture its output. The details vary by module, but significant amounts of the code are the same, and are abstracted into this package. Modules wrapping specific tools are provided in the net.sourceforge.seqware.pipeline.modules packages, and sub-packages. To create their own modules, users are expected to extend the Module class or the GenericCommandRunnerclass. the [TODO-Link] HelloWorld module provides an illustrative example.