Index

A

abspath (WDL.Tree.ReadSourceResult attribute) after (WDL.Tree.Call attribute) aliases (WDL.Tree.DocImport attribute) alternative (WDL.Expr.IfThenElse attribute) Any (class in WDL.Type) Apply (class in WDL.Expr)

arguments (WDL.Expr.Apply attribute) Array (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) available_inputs (WDL.Tree.Call property) (WDL.Tree.Task property) (WDL.Tree.Workflow property)

B

Base (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) bind() (WDL.Env.Bindings method) Binding (class in WDL.Env) Bindings (class in WDL.Env)

body (WDL.Tree.Workflow attribute) (WDL.Tree.WorkflowSection attribute) Boolean (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) build() (in module WDL.Zip)

C

Call (class in WDL.Tree) callee (WDL.Tree.Call attribute) callee_id (WDL.Tree.Call attribute) check() (WDL.Type.Base method) children (WDL.Error.SourceNode property) (WDL.Expr.Apply property) (WDL.Expr.Array property) (WDL.Expr.Get property) (WDL.Expr.Ident property) (WDL.Expr.IfThenElse property) (WDL.Expr.Map property) (WDL.Expr.Pair property) (WDL.Expr.Placeholder property) (WDL.Expr.String property) (WDL.Expr.Struct property)

CircularDependencies coerce() (WDL.Value.Base method) coerces() (WDL.Type.Base method) command (WDL.Tree.Task attribute) comparable() (WDL.Type.Base method) complete_calls (WDL.Tree.Workflow attribute) condition (WDL.Expr.IfThenElse attribute) Conditional (class in WDL.Tree) ConfigMissing consequent (WDL.Expr.IfThenElse attribute) copy() (WDL.Type.Array method) (WDL.Type.Base method)

D

Decl (class in WDL.Tree) decor (WDL.Tree.Decl attribute) digest (WDL.Tree.Task property) (WDL.Tree.Workflow property) digest_env() (in module WDL.Value)

dir (WDL.Zip.UnpackedZip attribute) Directory (class in WDL.Type) (class in WDL.Value) doc (WDL.Tree.DocImport attribute) DocImport (class in WDL.Tree) Document (class in WDL.Tree)

E

effective_outputs (WDL.Tree.Call property) (WDL.Tree.Task property) (WDL.Tree.Workflow property) effective_wdl_version (WDL.Tree.Document attribute) (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute) EmptyArray enter_namespace() (WDL.Env.Bindings method) equatable() (WDL.Type.Any method) (WDL.Type.Array method) (WDL.Type.Base method) (WDL.Type.Float method) (WDL.Type.Int method) (WDL.Type.Map method) (WDL.Type.Pair method) (WDL.Type.StructInstance method)

eval() (WDL.Expr.Base method) EvalError exceptions (WDL.Error.MultipleValidationErrors attribute) expect() (WDL.Value.Base method) expr (WDL.Expr.Get attribute) (WDL.Expr.Placeholder attribute) (WDL.Tree.Conditional attribute) (WDL.Tree.Decl attribute) (WDL.Tree.Scatter attribute) (WDL.Value.Base property)

F

File (class in WDL.Type) (class in WDL.Value) filter() (WDL.Env.Bindings method) final_referee (WDL.Tree.Gather property)

Float (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) from_json() (in module WDL.Value) function_name (WDL.Expr.Apply attribute)

G

Gather (class in WDL.Tree) gathers (WDL.Tree.WorkflowSection attribute)

Get (class in WDL.Expr) get() (WDL.Env.Bindings method) get_node() (WDL.Tree.Workflow method)

H

has_binding() (WDL.Env.Bindings method)

has_namespace() (WDL.Env.Bindings method)

I

Ident (class in WDL.Expr) IfThenElse (class in WDL.Expr) imported (WDL.Tree.StructTypeDef attribute) ImportError imports (WDL.Tree.Document attribute) IncompatibleOperand IndeterminateType infer_type() (WDL.Expr.Base method) info (WDL.Env.Binding property) input_file (WDL.Zip.UnpackedZip attribute) InputError

inputs (WDL.Tree.Call attribute) (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute) Int (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) InvalidType item_type (WDL.Type.Array attribute) (WDL.Type.Map attribute) items (WDL.Expr.Array attribute) (WDL.Expr.Map attribute)

J

json (WDL.Value.Base property)

L

left (WDL.Expr.Pair attribute) left_type (WDL.Type.Pair attribute) literal (WDL.Expr.Array property) (WDL.Expr.Base property) (WDL.Expr.Map property) (WDL.Expr.Pair property) (WDL.Expr.String property) (WDL.Expr.Struct property)

literal_keys (WDL.Type.Map attribute) load() (in module WDL) load_async() (in module WDL) Loader (class in WDL.runtime.config) log_all() (WDL.runtime.config.Loader method) log_unused_options() (WDL.runtime.config.Loader method)

M

main_wdl (WDL.Zip.UnpackedZip attribute) Map (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) map() (WDL.Env.Bindings method) member (WDL.Expr.Get attribute) members (WDL.Expr.Struct attribute) (WDL.Tree.StructTypeDef attribute) (WDL.Type.StructInstance attribute) merge() (in module WDL.Env) meta (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute) module WDL WDL.Env WDL.Error WDL.Expr WDL.Lint WDL.runtime WDL.runtime.config WDL.Tree WDL.Type WDL.Value WDL.Zip

more_info (WDL.Error.EmptyArray attribute) (WDL.Error.InputError attribute) (WDL.Error.NullValue attribute) (WDL.Error.OutOfBounds attribute) (WDL.Error.RuntimeError attribute) MultiLineString (class in WDL.Expr) MultipleDefinitions MultipleValidationErrors

N

name (WDL.Env.Binding property) (WDL.Expr.Ident attribute) (WDL.Tree.Call attribute) (WDL.Tree.Decl attribute) (WDL.Tree.StructTypeDef attribute) (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute) namespace (WDL.Tree.DocImport attribute) namespaces (WDL.Env.Bindings property) node (WDL.Error.EvalError attribute) (WDL.Error.ValidationError attribute)

nonempty (WDL.Type.Array property) NoSuchCall NoSuchFunction NoSuchInput NoSuchMember NoSuchTask NotAnArray Null (class in WDL.Expr) (class in WDL.Value) NullValue

O

optional (WDL.Type.Base property) options (WDL.Expr.Placeholder attribute)

OutOfBounds outputs (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute)

P

Pair (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) parameter_meta (WDL.Tree.Task attribute) (WDL.Tree.Workflow attribute) parameters (WDL.Type.Array property) (WDL.Type.Base property) (WDL.Type.Map property) (WDL.Type.Pair property) (WDL.Type.StructInstance property) parent (WDL.Error.SourceNode attribute) parts (WDL.Expr.MultiLineString attribute) (WDL.Expr.String attribute) (WDL.Expr.TaskCommand attribute) Placeholder (class in WDL.Expr) plugin_defaults() (WDL.runtime.config.Loader method) pos (WDL.Error.CircularDependencies attribute) (WDL.Error.EmptyArray attribute) (WDL.Error.EvalError attribute) (WDL.Error.IncompatibleOperand attribute) (WDL.Error.IndeterminateType attribute) (WDL.Error.InvalidType attribute) (WDL.Error.MultipleDefinitions attribute) (WDL.Error.NoSuchCall attribute) (WDL.Error.NoSuchFunction attribute) (WDL.Error.NoSuchInput attribute) (WDL.Error.NoSuchMember attribute) (WDL.Error.NoSuchTask attribute) (WDL.Error.NotAnArray attribute) (WDL.Error.NullValue attribute) (WDL.Error.OutOfBounds attribute) (WDL.Error.SourceNode attribute) (WDL.Error.StrayInputDeclaration attribute) (WDL.Error.UncallableWorkflow attribute) (WDL.Error.UnknownIdentifier attribute) (WDL.Error.ValidationError attribute) (WDL.Error.WrongArity attribute) (WDL.Expr.MultiLineString attribute) (WDL.Expr.TaskCommand attribute) (WDL.Tree.DocImport attribute) (WDL.Tree.SourceComment attribute)

postinputs (WDL.Tree.Task attribute)

R

read_source_default() (in module WDL) ReadSourceResult (class in WDL.Tree) referee (WDL.Expr.Ident attribute) (WDL.Tree.Gather attribute) required_inputs (WDL.Tree.Call property) (WDL.Tree.Task property) (WDL.Tree.Workflow property) resolve() (WDL.Env.Bindings method) resolve_binding() (WDL.Env.Bindings method)

resolve_file_import() (in module WDL) rewrite_env_files() (in module WDL.Value) rewrite_env_paths() (in module WDL.Value) rewrite_files() (in module WDL.Value) rewrite_paths() (in module WDL.Value) right (WDL.Expr.Pair attribute) right_type (WDL.Type.Pair attribute) run() (in module WDL.runtime) runtime (WDL.Tree.Task attribute) RuntimeError

S

Scatter (class in WDL.Tree) scatter_depth (WDL.Tree.WorkflowNode attribute) section (WDL.Tree.Gather attribute) source_comments (WDL.Tree.Document attribute) source_lines (WDL.Tree.Document attribute) source_text (WDL.Error.ValidationError attribute) (WDL.Tree.Document attribute) (WDL.Tree.ReadSourceResult attribute) SourceComment (class in WDL.Tree) SourceNode (class in WDL.Error) SourcePosition (class in WDL.Error) StaticTypeMismatch

StrayInputDeclaration String (class in WDL.Expr) (class in WDL.Type) (class in WDL.Value) Struct (class in WDL.Expr) (class in WDL.Value) struct_type_name (WDL.Expr.Struct attribute) struct_typedefs (WDL.Tree.Document attribute) StructInstance (class in WDL.Type) StructTypeDef (class in WDL.Tree) subtract() (WDL.Env.Bindings method) SyntaxError

T

Task (class in WDL.Tree) TaskCommand (class in WDL.Expr) tasks (WDL.Tree.Document attribute) text (WDL.Tree.SourceComment attribute) type (WDL.Expr.Base property) (WDL.Tree.Decl attribute) (WDL.Value.Array attribute) (WDL.Value.Base attribute) (WDL.Value.Boolean attribute) (WDL.Value.Directory attribute) (WDL.Value.File attribute) (WDL.Value.Float attribute) (WDL.Value.Int attribute) (WDL.Value.Map attribute) (WDL.Value.Null attribute) (WDL.Value.Pair attribute) (WDL.Value.String attribute)

type_id (WDL.Tree.StructTypeDef property) (WDL.Type.StructInstance property) type_name (WDL.Type.StructInstance attribute) typecheck() (WDL.Expr.Base method) (WDL.Tree.Document method)

U

UncallableWorkflow unify() (in module WDL.Type) UnknownIdentifier

unpack() (in module WDL.Zip) UnpackedZip (class in WDL.Zip) uri (WDL.Tree.DocImport attribute)

V

ValidationError value (WDL.Env.Binding property) (WDL.Expr.Boolean attribute) (WDL.Expr.Float attribute) (WDL.Expr.Int attribute) (WDL.Expr.Null attribute) (WDL.Value.Array attribute) (WDL.Value.Base attribute) (WDL.Value.Boolean attribute) (WDL.Value.Directory attribute) (WDL.Value.File attribute) (WDL.Value.Float attribute) (WDL.Value.Int attribute) (WDL.Value.Map attribute) (WDL.Value.Null attribute) (WDL.Value.Pair attribute) (WDL.Value.String attribute) (WDL.Value.Struct attribute)

values_from_json() (in module WDL) values_to_json() (in module WDL) variable (WDL.Tree.Scatter attribute)

W

WDL module WDL.Env module WDL.Error module WDL.Expr module WDL.Lint module WDL.runtime module WDL.runtime.config module WDL.Tree module

WDL.Type module WDL.Value module WDL.Zip module wdl_version (WDL.Tree.Document attribute) Workflow (class in WDL.Tree) workflow (WDL.Tree.Document attribute) workflow_node_dependencies (WDL.Tree.WorkflowNode property) workflow_node_id (WDL.Tree.WorkflowNode attribute) WorkflowNode (class in WDL.Tree) WorkflowSection (class in WDL.Tree) wrap_namespace() (WDL.Env.Bindings method) WrongArity