| Package | Description |
|---|---|
| net.sourceforge.seqware.pipeline.module |
This package provides the SeqWare module interface and API, including
common code and classes.
|
| net.sourceforge.seqware.pipeline.modules |
Executables that can be called by workflows and users.
|
| net.sourceforge.seqware.pipeline.modules.utilities |
Modules that are used by workflows.
|
| net.sourceforge.seqware.pipeline.runner |
Runs plugins and modules.
|
| Modifier and Type | Class and Description |
|---|---|
class |
TestModule
This is an empty module mainly for testing purpose.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GenericCommandRunner
This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command
is specified.
|
class |
GenericMetadataSaver
Deprecated.
Deprecating this in favour of Metadata(plugin) and the new CLI
|
| Modifier and Type | Class and Description |
|---|---|
class |
ProvisionDependenciesBundle
Purpose:
This module takes a software bundle and unzips it to the temporary directory.
|
class |
ProvisionFiles
Purpose:
This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket
URL, HTTP/HTTPS URL, or local directory path).
|
class |
S3CreateFileURLs
Purpose:
This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.
|
class |
S3DeleteFiles
Purpose:
This module simply lists files at the S3 URL you provide.
|
class |
S3ListFiles
Purpose:
This module simply lists files at the S3 URL you provide.
|
class |
S3UploadDirectory
Purpose:
This module uses the Amazon API to recursively upload a directory to an S3 bucket.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Runner.evaluateReturn(Module app,
String methodName)
evaluateReturn.
|
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