Index

A

assemble_macro_matrix() (in module blue_cwl.connectome) assemble_micro_matrix() (in module blue_cwl.connectome)

atlas_densities_composition_summary() (in module blue_cwl.statistics) AtlasInfo (class in blue_cwl.staging)

B

baseCommand (blue_cwl.core.cwl.CommandLineTool attribute) blue_cwl module blue_cwl.connectome module blue_cwl.core module blue_cwl.core.command module blue_cwl.core.common module blue_cwl.core.config module blue_cwl.core.cwl module blue_cwl.core.cwl_types module blue_cwl.core.environment module blue_cwl.core.executor module blue_cwl.core.parser module blue_cwl.core.resolve module

blue_cwl.density_manipulation module blue_cwl.nexus module blue_cwl.population_utils module blue_cwl.recipes module blue_cwl.registering module blue_cwl.staging module blue_cwl.statistics module blue_cwl.variant module build_cell_composition_from_me_densities() (in module blue_cwl.recipes) build_command() (blue_cwl.core.executor.Executor method) (blue_cwl.core.executor.SallocExecutor method) build_connectome_distance_dependent_recipe() (in module blue_cwl.recipes) build_connectome_manipulator_recipe() (in module blue_cwl.recipes) build_environment_command() (in module blue_cwl.core.environment) build_mtype_taxonomy() (in module blue_cwl.recipes) build_salloc_command() (in module blue_cwl.core.command)

C

checksum (blue_cwl.core.cwl_types.File property) CommandInputArraySchema (class in blue_cwl.core.cwl) CommandInputParameter (class in blue_cwl.core.cwl) CommandLineBinding (class in blue_cwl.core.cwl) CommandLineTool (class in blue_cwl.core.cwl) CommandOutputBinding (class in blue_cwl.core.cwl) CommandOutputParameter (class in blue_cwl.core.cwl)

Config (class in blue_cwl.core.config) (class in blue_cwl.core.cwl) ConfigInput (class in blue_cwl.core.cwl) Constants (class in blue_cwl.connectome) contents (blue_cwl.core.cwl_types.File property) CustomBaseModel (class in blue_cwl.core.common) cwlVersion (blue_cwl.core.cwl.Workflow attribute) CWLWorkflowType (class in blue_cwl.core.cwl_types)

D

definition (blue_cwl.Variant property) (blue_cwl.variant.Variant property) density_manipulation() (in module blue_cwl.density_manipulation)

density_summary_stats_region() (in module blue_cwl.statistics) Directory (class in blue_cwl.core.cwl_types) dirname (blue_cwl.core.cwl_types.File property) download_distribution() (in module blue_cwl.nexus)

E

evolve() (blue_cwl.Variant method) (blue_cwl.variant.Variant method)

Executor (class in blue_cwl.core.executor)

F

File (class in blue_cwl.core.cwl_types) forge_to_config() (in module blue_cwl.nexus) from_dict() (blue_cwl.core.common.CustomBaseModel class method) from_file() (blue_cwl.staging.AtlasInfo class method) (blue_cwl.Variant class method) (blue_cwl.variant.Variant class method)

from_id() (blue_cwl.Variant class method) (blue_cwl.variant.Variant class method) from_registry() (blue_cwl.Variant class method) (blue_cwl.variant.Variant class method) from_search() (blue_cwl.Variant class method) (blue_cwl.variant.Variant class method) from_string() (blue_cwl.core.common.CustomBaseModel class method)

G

get_content() (blue_cwl.Variant method) (blue_cwl.variant.Variant method) get_distribution() (in module blue_cwl.nexus) get_distribution_as_dict() (in module blue_cwl.nexus) get_distribution_location_path() (in module blue_cwl.nexus) get_entry_id() (in module blue_cwl.staging) get_forge() (in module blue_cwl.nexus)

get_HRM_counts() (in module blue_cwl.population_utils) get_HRM_positions() (in module blue_cwl.population_utils) get_pathways() (in module blue_cwl.population_utils) get_region_acronym() (in module blue_cwl.nexus) get_resource() (in module blue_cwl.nexus) get_statistics_from_nrrd_volume() (in module blue_cwl.statistics) get_step_by_name() (blue_cwl.core.cwl.Workflow method) get_step_source_names() (blue_cwl.core.cwl.Workflow method)

I

id (blue_cwl.core.cwl.CommandLineTool attribute) (blue_cwl.core.cwl.Workflow attribute) (blue_cwl.core.cwl.WorkflowStep attribute) InputArraySchema (class in blue_cwl.core.cwl)

inputs (blue_cwl.core.cwl.CommandLineTool attribute) (blue_cwl.core.cwl.WorkflowStep attribute) iter_registered_variants() (in module blue_cwl.variant) iter_steps() (blue_cwl.core.cwl.Workflow method)

L

label (blue_cwl.core.cwl.CommandLineTool attribute) (blue_cwl.core.cwl.Workflow attribute)

LocalExecutor (class in blue_cwl.core.executor)

M

make() (blue_cwl.core.cwl.CommandLineTool method) (blue_cwl.core.cwl.Workflow method) make_workflow_step() (blue_cwl.core.cwl.Workflow method) materialize_cell_composition_summary() (in module blue_cwl.staging) materialize_cell_composition_volume() (in module blue_cwl.staging) materialize_density_distribution() (in module blue_cwl.staging) materialize_macro_connectome_config() (in module blue_cwl.staging) materialize_micro_connectome_config() (in module blue_cwl.staging) materialize_ph_catalog() (in module blue_cwl.staging) materialize_synapse_config() (in module blue_cwl.staging) model_config (blue_cwl.core.common.CustomBaseModel attribute) (blue_cwl.core.config.Config attribute) (blue_cwl.core.config.RemoteConfig attribute) (blue_cwl.core.config.SlurmConfig attribute) (blue_cwl.core.cwl.CommandInputArraySchema attribute) (blue_cwl.core.cwl.CommandInputParameter attribute) (blue_cwl.core.cwl.CommandLineBinding attribute) (blue_cwl.core.cwl.CommandLineTool attribute) (blue_cwl.core.cwl.CommandOutputBinding attribute) (blue_cwl.core.cwl.CommandOutputParameter attribute) (blue_cwl.core.cwl.Config attribute) (blue_cwl.core.cwl.ConfigInput attribute) (blue_cwl.core.cwl.InputArraySchema attribute) (blue_cwl.core.cwl.Workflow attribute) (blue_cwl.core.cwl.WorkflowInputParameter attribute) (blue_cwl.core.cwl.WorkflowOutputParameter attribute) (blue_cwl.core.cwl.WorkflowStep attribute) (blue_cwl.core.cwl.WorkflowStepInput attribute) (blue_cwl.core.cwl_types.Directory attribute) (blue_cwl.core.cwl_types.File attribute) (blue_cwl.core.cwl_types.NexusResource attribute) (blue_cwl.core.executor.Executor attribute) (blue_cwl.core.executor.LocalExecutor attribute) (blue_cwl.core.executor.RemoteExecutor attribute) (blue_cwl.core.executor.SallocExecutor attribute)

module blue_cwl blue_cwl.connectome blue_cwl.core blue_cwl.core.command blue_cwl.core.common blue_cwl.core.config blue_cwl.core.cwl blue_cwl.core.cwl_types blue_cwl.core.environment blue_cwl.core.executor blue_cwl.core.parser blue_cwl.core.resolve blue_cwl.density_manipulation blue_cwl.nexus blue_cwl.population_utils blue_cwl.recipes blue_cwl.registering blue_cwl.staging blue_cwl.statistics blue_cwl.variant mtype_etype_url_mapping() (in module blue_cwl.statistics) mtype_etype_url_mapping_from_nexus() (in module blue_cwl.statistics)

N

nameext (blue_cwl.core.cwl_types.File property) nameroot (blue_cwl.core.cwl_types.File property)

NexusResource (class in blue_cwl.core.cwl_types) node_population_composition_summary() (in module blue_cwl.statistics)

O

outputs (blue_cwl.core.cwl.CommandLineTool attribute) (blue_cwl.core.cwl.WorkflowStep attribute)

outputSource (blue_cwl.core.cwl.WorkflowOutputParameter attribute) overview (blue_cwl.Variant property) (blue_cwl.variant.Variant property)

P

parse_config_file() (in module blue_cwl.core.parser) parse_cwl_data() (in module blue_cwl.core.parser) parse_cwl_file() (in module blue_cwl.core) (in module blue_cwl.core.parser)

position (blue_cwl.core.cwl.CommandLineBinding attribute) prefix (blue_cwl.core.cwl.CommandLineBinding attribute) publish() (blue_cwl.Variant method) (blue_cwl.variant.Variant method)

R

read_density_manipulation_recipe() (in module blue_cwl.density_manipulation) register_cell_composition() (in module blue_cwl.registering) register_cell_composition_summary() (in module blue_cwl.registering) register_cell_composition_volume() (in module blue_cwl.registering) register_densities() (in module blue_cwl.registering) register_partial_circuit() (in module blue_cwl.registering) RemoteConfig (class in blue_cwl.core.config)

RemoteExecutor (class in blue_cwl.core.executor) resolve_micro_matrices() (in module blue_cwl.connectome) resolve_parameter_references() (in module blue_cwl.core.resolve) run (blue_cwl.core.cwl.WorkflowStep attribute) run() (blue_cwl.core.executor.Executor method) (blue_cwl.core.executor.LocalExecutor method) (blue_cwl.core.executor.RemoteExecutor method) run_command() (in module blue_cwl.core.command)

S

SallocExecutor (class in blue_cwl.core.executor) search_variant_in_nexus() (in module blue_cwl.variant) show_image() (blue_cwl.core.cwl.Workflow method) size (blue_cwl.core.cwl_types.File property) SlurmConfig (class in blue_cwl.core.config) split_source_output() (blue_cwl.core.cwl.WorkflowOutputParameter method) (blue_cwl.core.cwl.WorkflowStepInput method)

stage_atlas() (in module blue_cwl.staging) stage_detailed_circuit() (in module blue_cwl.staging) stage_distribution_file() (in module blue_cwl.staging) stage_file() (in module blue_cwl.staging) stage_variant() (in module blue_cwl.staging) stdout (blue_cwl.core.cwl.CommandLineTool attribute) step_names() (blue_cwl.core.cwl.Workflow method)

T

to_command_parameters() (blue_cwl.core.config.SlurmConfig method) to_dict() (blue_cwl.core.common.CustomBaseModel method) to_file() (blue_cwl.staging.AtlasInfo method) to_json() (blue_cwl.core.common.CustomBaseModel method) to_string() (blue_cwl.core.common.CustomBaseModel method)

tool_definition (blue_cwl.Variant property) (blue_cwl.variant.Variant property) transform_cached() (in module blue_cwl.staging) transform_nested_dataset() (in module blue_cwl.staging) type (blue_cwl.core.cwl.WorkflowOutputParameter attribute)

U

update() (blue_cwl.core.config.Config method)

V

Variant (class in blue_cwl) (class in blue_cwl.variant)

W

Workflow (class in blue_cwl.core.cwl) WorkflowInputParameter (class in blue_cwl.core.cwl) WorkflowOutputParameter (class in blue_cwl.core.cwl)

WorkflowStep (class in blue_cwl.core.cwl) WorkflowStepInput (class in blue_cwl.core.cwl) write_functionalizer_json_recipe() (in module blue_cwl.recipes) write_image() (blue_cwl.core.cwl.Workflow method)