Janis
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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
Janis Prepare
Expressions
Scattering
Secondary / Accessory Files
Unit Test Framework
Guides
Configuring Janis Assistant
Configuring resources (CPU / Memory)
Call Caching
Common Workflow Language
Workflow Description Language
Collecting tool outputs
Configuring Janis for HPCs
Engine support
Updating Janis
Frequently asked questions
Common errors
Parsing CWL
Development
Development
Contributing
Testing
Releasing Janis
Janis
Docs
»
Index
Edit on GitHub
Index
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__init__() (janis.CommandToolBuilder method)
(janis.InputDocumentation method)
(janis.ScatterDescription method)
(janis.ToolArgument method)
(janis.ToolInput method)
(janis.ToolOutput method)
,
[1]
(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)
InputDocumentation (class in janis)
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)
,
[1]
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)