Janis
latest
Welcome to Janis!
About
Pipeline concepts
Tutorials
Tutorial 0 - Introduction to Janis
Tutorial 1 - Building a Workflow
Tutorial 2 - Wrapping a new tool
Tutorial 3 - Naming and organising outputs
Adding a tool to a toolbox
Running your workflow
Containerising a tool
Shed / Toolbox
Pipelines
Tools
Data Types
Templates
List of operators
Janis Shed and Toolboxes
API documentation
Framework Documentation
Workflow
Command Tool
Python Tool
Expressions
Scattering
Secondary / Accessory Files
Unit Test Framework
Guides
Configuring Janis Assistant
Configuring resources (CPU / Memory)
Call Caching
Common Workflow Language
Workflow Description Language
Engine support
Updating Janis
Frequently asked questions
Common errors
Development
Development
Contributing
Testing
Releasing Janis
Janis
Docs
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Index
Edit on GitHub
Index
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C
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_
__init__() (janis.CommandToolBuilder method)
(janis.ScatterDescription method)
(janis.ToolArgument method)
(janis.ToolInput method)
(janis.ToolOutput method)
(janis_assistant.management.configuration.JanisConfiguration method)
(janis_assistant.management.configuration.JanisConfigurationCromwell method)
(janis_assistant.management.configuration.JanisConfigurationEnvironment method)
(janis_assistant.management.configuration.JanisConfigurationNotifications method)
(janis_assistant.management.configuration.JanisConfigurationRecipes method)
(janis_assistant.management.configuration.JanisConfigurationTemplate method)
(janis_assistant.management.configuration.MySqlInstanceConfig method)
B
bind_metadata() (janis.Workflow method)
Boolean (class in janis)
C
code_block() (janis.PythonTool static method)
CommandTool (class in janis)
CommandToolBuilder (class in janis)
config_dir (janis_assistant.management.envvariables.EnvVariables attribute)
config_path (janis_assistant.management.envvariables.EnvVariables attribute)
constructor() (janis.DynamicWorkflow method)
(janis.Workflow method)
cromwelljar (janis_assistant.management.envvariables.EnvVariables attribute)
D
default_template (janis_assistant.management.envvariables.EnvVariables attribute)
DynamicWorkflow (class in janis)
E
EnvVariables (class in janis_assistant.management.envvariables)
exec_dir (janis_assistant.management.envvariables.EnvVariables attribute)
F
File (class in janis)
Filename (class in janis)
Float (class in janis)
friendly_name() (janis.Workflow method)
I
id() (janis.Workflow method)
input() (janis.Workflow method)
InputSelector (class in janis)
Int (class in janis)
J
JanisConfiguration (class in janis_assistant.management.configuration)
JanisConfigurationCromwell (class in janis_assistant.management.configuration)
JanisConfigurationEnvironment (class in janis_assistant.management.configuration)
JanisConfigurationNotifications (class in janis_assistant.management.configuration)
JanisConfigurationRecipes (class in janis_assistant.management.configuration)
JanisConfigurationTemplate (class in janis_assistant.management.configuration)
M
modify_inputs() (janis.DynamicWorkflow method)
MySqlInstanceConfig (class in janis_assistant.management.configuration)
O
output() (janis.Workflow method)
output_dir (janis_assistant.management.envvariables.EnvVariables attribute)
P
PythonTool (class in janis)
R
recipe_directory (janis_assistant.management.envvariables.EnvVariables attribute)
recipe_paths (janis_assistant.management.envvariables.EnvVariables attribute)
S
ScatterDescription (class in janis)
ScatterMethods (in module janis)
search_path (janis_assistant.management.envvariables.EnvVariables attribute)
step() (janis.Workflow method)
String (class in janis)
StringFormatter (class in janis)
T
ToolArgument (class in janis)
ToolInput (class in janis)
ToolOutput (class in janis)
translate() (janis.Workflow method)
TTestCase (class in janis_core.tool.test_classes)
TTestExpectedOutput (class in janis_core.tool.test_classes)
TTestPreprocessor (class in janis_core.tool.test_classes)
W
WildcardSelector (class in janis)
Workflow (class in janis)
WorkflowBuilder (class in janis)
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