| Package | Description |
|---|---|
| io.seqware.pipeline.plugins |
Newly written SeqWare plugins
|
| io.seqware.pipeline.plugins.sanity |
Base classes for the sanity check tool.
|
| net.sourceforge.seqware.pipeline.deciders |
BasicDecider.
|
| net.sourceforge.seqware.pipeline.plugin |
Interface for plugins and the workflow launcher for some reason.
|
| net.sourceforge.seqware.pipeline.plugins |
Create and manipulate databases for extended testing.
|
| net.sourceforge.seqware.pipeline.plugins.checkdb |
Check the metadb for errors in convention and structure.
|
| net.sourceforge.seqware.pipeline.plugins.deletion |
Implementation for the deletion tool that can delete workflow runs.
|
| net.sourceforge.seqware.pipeline.plugins.fileprovenance |
Dump out the file provenance report to the user.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FileProvenanceQueryTool
Pulls back a file provenance report, runs an arbitrarily complex SQL query on the results, and saves the results as a protobuf binary for
use as a part of interpreted language deciders.
|
class |
UserSettingsPlugin
This plugin outputs a commented config file
|
class |
WorkflowLauncher
The WorkflowLauncher is responsible for launching scheduled workflows.
|
class |
WorkflowLifecycle
The WorkflowLifecycle is responsible for performing aggregations of tasks.
|
class |
WorkflowRelauncher
The Workflow relauncher is only responsible for relaunching failed workflows.
|
class |
WorkflowRescheduler
The Workflow Rescheduler can schedule a new workflow based on the configuration of a previously launched workflow.
|
class |
WorkflowScheduler
The Workflow Scheduler is only responsible for scheduling workflows.
|
class |
WorkflowWatcher
The Workflow Watcher is only responsible for watching workflows and reporting on their status in a real-time manner.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SanityCheck
A database validation tool for your SeqWare metadb
|
| Modifier and Type | Class and Description |
|---|---|
class |
BasicDecider |
| Modifier and Type | Class and Description |
|---|---|
class |
Plugin
Abstract Plugin class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AttributeAnnotator
AttributeAnnotator class.
|
class |
BatchMetadataInjection
BatchImport class.
|
class |
BundleManager
BundleManager class.
|
class |
CycleChecker
CycleChecker class.
|
class |
FileLinker
FileLinker class.
|
class |
HelloWorld
HelloWorld class.
|
class |
MarkdownPlugin
This plugin outputs documentation for our plugins and modules in markdown format
|
class |
Metadata
This plugin currently lets users creation a limited set of table rows in the database from the command line.
|
class |
ModuleRunner
ModuleRunner class.
|
class |
OozieXML2Dot |
class |
ProcessingDataStructure2Dot |
class |
WorkflowRunFilesInitialPopulationPlugin
This plugin does the initial population of workflow run files in order to track input files when migrating from SeqWare 0.13.6.X to
1.0.X.
|
class |
WorkflowRunReporter
WorkflowRunReporter class.
|
class |
WorkflowStatusChecker
This plugin lets you monitor the status of running workflows and updates the metadata object with their status.
|
| Modifier and Type | Method and Description |
|---|---|
int |
MarkdownPlugin.PluginComparator.compare(PluginInterface t,
PluginInterface t1) |
| Modifier and Type | Class and Description |
|---|---|
class |
CheckDB
A database validation tool for your SeqWare metadb
|
| Modifier and Type | Class and Description |
|---|---|
class |
DeletionDB
A workflow run deletion tool for your SeqWare metadb
|
| Modifier and Type | Class and Description |
|---|---|
class |
FileProvenanceReporter
Lightweight wrapper for file provenance report
|
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