Index

_

__init__() (sophios.apis.python.tool_builder.CommandArgument method) (sophios.apis.python.tool_builder.CommandLineBinding method) (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.CommandOutputBinding method) (sophios.apis.python.tool_builder.Dirent method) (sophios.apis.python.tool_builder.DockerRequirement method) (sophios.apis.python.tool_builder.EnvironmentDef method) (sophios.apis.python.tool_builder.EnvVarRequirement method) (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InitialWorkDirRequirement method) (sophios.apis.python.tool_builder.InlineJavascriptRequirement method) (sophios.apis.python.tool_builder.InplaceUpdateRequirement method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.LoadListingRequirement method) (sophios.apis.python.tool_builder.NetworkAccess method) (sophios.apis.python.tool_builder.OutputSpec method) (sophios.apis.python.tool_builder.ResourceRequirement method) (sophios.apis.python.tool_builder.SchemaDefRequirement method) (sophios.apis.python.tool_builder.SecondaryFile method) (sophios.apis.python.tool_builder.ShellCommandRequirement method) (sophios.apis.python.tool_builder.SoftwarePackage method) (sophios.apis.python.tool_builder.SoftwareRequirement method) (sophios.apis.python.tool_builder.ToolTimeLimit method) (sophios.apis.python.tool_builder.ValidationResult method) (sophios.apis.python.tool_builder.WorkReuse method) (sophios.apis.python.workflow.Step method) (sophios.apis.python.workflow.Workflow method) (sophios.compute_payload.ComputeConfig method) (sophios.compute_payload.ComputeWorkflowPayload method) (sophios.compute_payload.OutputConfig method) (sophios.compute_payload.SlurmConfig method) (sophios.compute_payload.ToilConfig method) (sophios.wic_types.GraphData method)

A

absolute_paths() (in module sophios.cwl_subinterpreter) add_argument() (sophios.apis.python.tool_builder.CommandLineTool method) add_graph_edge() (in module sophios.utils_graphs) add_input() (sophios.apis.python.workflow.Workflow method) add_output() (sophios.apis.python.workflow.Workflow method) add_subgraphs() (in module sophios.utils_graphs) add_yamldict_keyval_in() (in module sophios.utils_cwl) add_yamldict_keyval_out() (in module sophios.utils_cwl)

alias_constructor() (in module sophios.utils_yaml) anchor_constructor() (in module sophios.utils_yaml) append() (sophios.apis.python.workflow.Workflow method) apply_args() (in module sophios.inlineing) argument() (sophios.apis.python.tool_builder.CommandLineTool method) array() (sophios.apis.python.tool_builder.FieldSpec class method) (sophios.apis.python.tool_builder.InputSpec class method) (sophios.apis.python.tool_builder.OutputSpec class method) array_type() (in module sophios.apis.python.tool_builder)

B

base_command() (sophios.apis.python.tool_builder.CommandLineTool method) bind_input() (sophios.apis.python.workflow.Step method) (sophios.apis.python.workflow.Workflow method) bind_output() (sophios.apis.python.workflow.Workflow method) binding (sophios.apis.python.tool_builder.CommandArgument attribute)

binding_extra (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) binding_value_from (sophios.apis.python.tool_builder.InputSpec attribute) build() (sophios.apis.python.tool_builder.CommandLineTool method) build_cmd() (in module sophios.run_local)

C

canonicalize_inputs_dict() (in module sophios.utils_cwl) canonicalize_outputs_dict() (in module sophios.utils_cwl) canonicalize_steps_dict() (in module sophios.utils_cwl) canonicalize_steps_list() (in module sophios.utils_cwl) canonicalize_type() (in module sophios.utils_cwl) cfg_yaml (sophios.apis.python.workflow.Step attribute) check_args_match_inputs() (in module sophios.python_cwl_adapter) class_name (sophios.apis.python.tool_builder.DockerRequirement attribute) (sophios.apis.python.tool_builder.EnvVarRequirement attribute) (sophios.apis.python.tool_builder.InitialWorkDirRequirement attribute) (sophios.apis.python.tool_builder.InlineJavascriptRequirement attribute) (sophios.apis.python.tool_builder.InplaceUpdateRequirement attribute) (sophios.apis.python.tool_builder.LoadListingRequirement attribute) (sophios.apis.python.tool_builder.NetworkAccess attribute) (sophios.apis.python.tool_builder.ResourceRequirement attribute) (sophios.apis.python.tool_builder.SchemaDefRequirement attribute) (sophios.apis.python.tool_builder.ShellCommandRequirement attribute) (sophios.apis.python.tool_builder.SoftwareRequirement attribute) (sophios.apis.python.tool_builder.ToolTimeLimit attribute) (sophios.apis.python.tool_builder.WorkReuse attribute) cli_watcher() (in module sophios.cwl_subinterpreter) clt (sophios.apis.python.workflow.Step attribute) clt_path (sophios.apis.python.workflow.Step attribute) CommandArgument (class in sophios.apis.python.tool_builder) CommandLineBinding (class in sophios.apis.python.tool_builder) CommandLineTool (class in sophios.apis.python.tool_builder) CommandOutputBinding (class in sophios.apis.python.tool_builder) compile() (sophios.apis.python.workflow.Workflow method) compile_workflow() (in module sophios.compiler)

compile_workflow_generate_schema() (in module sophios.schemas.wic_schema) compile_workflow_once() (in module sophios.compiler) compiled_cwl (sophios.wic_types.NodeData attribute) CompilerInfo (class in sophios.wic_types) compute_config (sophios.compute_payload.ComputeWorkflowPayload attribute) ComputeConfig (class in sophios.compute_payload) ComputePayloadValidationError ComputeWorkflowPayload (class in sophios.compute_payload) convert_args_dict_to_args_list() (in module sophios.utils) copy_cwl_input_output_dict() (in module sophios.utils_cwl) copy_output_files() (in module sophios.run_local) cores_max (sophios.apis.python.tool_builder.ResourceRequirement attribute) cores_min (sophios.apis.python.tool_builder.ResourceRequirement attribute) cpus_per_task (sophios.compute_payload.SlurmConfig attribute) create_safe_env() (in module sophios.run_local) cwl (sophios.wic_types.Tool attribute) cwl_job_inputs (sophios.compute_payload.ComputeWorkflowPayload attribute) cwl_prepend_dockerFile_include_path() (in module sophios.plugins) cwl_prepend_dockerFile_include_path_rosetree() (in module sophios.plugins) cwl_schema() (in module sophios.schemas.wic_schema) cwl_type_to_jsonschema_type() (in module sophios.schemas.wic_schema) cwl_type_to_jsonschema_type_schema() (in module sophios.schemas.wic_schema) cwl_update_outputs_optional() (in module sophios.plugins) cwl_update_outputs_optional_rosetree() (in module sophios.plugins) cwl_version (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.workflow.Step attribute) cwl_workflow (sophios.compute_payload.ComputeWorkflowPayload attribute) cwltool_main() (in module sophios.run_local) cwltool_main_pf() (in module sophios.run_local)

D

data (sophios.wic_types.RoseTree attribute) default() (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InputSpec method) default_schema() (in module sophios.schemas.wic_schema) default_value (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InputSpec attribute) describe() (sophios.apis.python.tool_builder.CommandLineTool method) desugar_into_canonical_normal_form() (in module sophios.utils_cwl) Dirent (class in sophios.apis.python.tool_builder) DisableEverythingFilter (class in sophios.apis.python.workflow) doc() (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method)

doc_text (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) docker() (sophios.apis.python.tool_builder.CommandLineTool method) docker_file (sophios.apis.python.tool_builder.DockerRequirement attribute) docker_image_id (sophios.apis.python.tool_builder.DockerRequirement attribute) docker_import (sophios.apis.python.tool_builder.DockerRequirement attribute) docker_load (sophios.apis.python.tool_builder.DockerRequirement attribute) docker_output_directory (sophios.apis.python.tool_builder.DockerRequirement attribute) docker_pull (sophios.apis.python.tool_builder.DockerRequirement attribute) dockerPull_append_noentrypoint() (in module sophios.plugins) dockerPull_append_noentrypoint_rosetree() (in module sophios.plugins) dockerPull_append_noentrypoint_tools() (in module sophios.plugins) DockerRequirement (class in sophios.apis.python.tool_builder)

E

edam() (sophios.apis.python.tool_builder.CommandLineTool method) enable_reuse (sophios.apis.python.tool_builder.WorkReuse attribute) entry (sophios.apis.python.tool_builder.Dirent attribute) entryname (sophios.apis.python.tool_builder.Dirent attribute) enum() (sophios.apis.python.tool_builder.FieldSpec class method) (sophios.apis.python.tool_builder.InputSpec class method) (sophios.apis.python.tool_builder.OutputSpec class method) enum_type() (in module sophios.apis.python.tool_builder) env (sophios.wic_types.CompilerInfo attribute) env_def (sophios.apis.python.tool_builder.EnvVarRequirement attribute) env_name (sophios.apis.python.tool_builder.EnvironmentDef attribute) env_value (sophios.apis.python.tool_builder.EnvironmentDef attribute) env_var() (sophios.apis.python.tool_builder.CommandLineTool method) EnvData (class in sophios.wic_types) EnvironmentDef (class in sophios.apis.python.tool_builder) EnvVarRequirement (class in sophios.apis.python.tool_builder) error (sophios.compute_payload.SlurmConfig attribute) explicit_edge_calls (sophios.wic_types.EnvData attribute) (sophios.wic_types.NodeData attribute) explicit_edge_defs (sophios.wic_types.EnvData attribute) (sophios.wic_types.NodeData attribute) expression_lib (sophios.apis.python.tool_builder.InlineJavascriptRequirement attribute) extra (sophios.apis.python.tool_builder.CommandArgument attribute) (sophios.apis.python.tool_builder.CommandLineBinding attribute) (sophios.apis.python.tool_builder.CommandOutputBinding attribute) (sophios.apis.python.tool_builder.Dirent attribute) (sophios.apis.python.tool_builder.DockerRequirement attribute) (sophios.apis.python.tool_builder.EnvVarRequirement attribute) (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InitialWorkDirRequirement attribute) (sophios.apis.python.tool_builder.InlineJavascriptRequirement attribute) (sophios.apis.python.tool_builder.InplaceUpdateRequirement attribute) (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.LoadListingRequirement attribute) (sophios.apis.python.tool_builder.NetworkAccess attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) (sophios.apis.python.tool_builder.ResourceRequirement attribute) (sophios.apis.python.tool_builder.SchemaDefRequirement attribute) (sophios.apis.python.tool_builder.SecondaryFile attribute) (sophios.apis.python.tool_builder.ShellCommandRequirement attribute) (sophios.apis.python.tool_builder.SoftwarePackage attribute) (sophios.apis.python.tool_builder.SoftwareRequirement attribute) (sophios.apis.python.tool_builder.ToolTimeLimit attribute) (sophios.apis.python.tool_builder.WorkReuse attribute)

extra() (sophios.apis.python.tool_builder.CommandLineTool method) extract_implementation() (in module sophios.utils)

F

Field (in module sophios.apis.python.tool_builder) FieldSpec (class in sophios.apis.python.tool_builder) file_watcher_glob() (in module sophios.cwl_subinterpreter) filter() (sophios.apis.python.workflow.DisableEverythingFilter method) (sophios.plugins.NoPartialFailureNullWarning method) (sophios.plugins.NoPreviouslyDefinedFilter method) (sophios.plugins.NoResolvedFilter method) flag (sophios.apis.python.tool_builder.InputSpec attribute) flatten() (in module sophios.utils) flatten_forest() (in module sophios.utils) flatten_graphdata() (in module sophios.utils_graphs)

flatten_rose_tree() (in module sophios.utils) flatten_steps() (sophios.apis.python.workflow.Step method) (sophios.apis.python.workflow.Workflow method) flatten_subworkflows() (sophios.apis.python.workflow.Step method) (sophios.apis.python.workflow.Workflow method) format() (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) format_value (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) from_cwl() (sophios.apis.python.workflow.Step class method) from_input() (sophios.apis.python.tool_builder.Dirent class method) from_json() (sophios.compute_payload.OutputConfig class method)

G

generate_CWL_CommandLineTool() (in module sophios.python_cwl_adapter) generate_run_script() (in module sophios.run_local) get_absolute_paths() (in module sophios.input_output) get_args() (in module sophios.cli) get_basic_config() (in module sophios.input_output) get_compute_payload() (sophios.compute_payload.ComputeWorkflowPayload method) get_config() (in module sophios.input_output) get_cwl_workflow() (sophios.apis.python.workflow.Workflow method) get_dicts_for_compilation() (in module sophios.cli) get_graph_reps() (in module sophios.utils_graphs) get_home_paths() (in module sophios.input_output) get_inference_rules() (in module sophios.inference) get_inlineable_subworkflows() (in module sophios.inlineing) get_inp_attr() (sophios.apis.python.workflow.Step method) (sophios.apis.python.workflow.Workflow method) get_input_mappings() (in module sophios.utils) get_inputs_workflow() (in module sophios.python_cwl_adapter) get_known_and_unknown_args() (in module sophios.cli) get_main_args() (in module sophios.python_cwl_adapter) get_module() (in module sophios.python_cwl_adapter)

get_output() (sophios.apis.python.workflow.Step method) get_output_mapping() (in module sophios.utils) get_py_paths() (in module sophios.plugins) get_step_name_1() (in module sophios.utils) get_steps_keys() (in module sophios.utils) get_subkeys() (in module sophios.utils) get_tools_cwl() (in module sophios.plugins) get_validator() (in module sophios.schemas.wic_schema) get_workflow_outputs() (in module sophios.utils_cwl) get_workflow_paths() (in module sophios.plugins) get_yml_paths() (in module sophios.plugins) glob (sophios.apis.python.tool_builder.CommandOutputBinding attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) gpu() (sophios.apis.python.tool_builder.CommandLineTool method) graph (sophios.wic_types.NodeData attribute) GraphData (class in sophios.wic_types) graphdata (sophios.wic_types.GraphReps attribute) graphdata_to_cytoscape() (in module sophios.utils_graphs) GraphReps (class in sophios.wic_types) graphviz (sophios.wic_types.GraphReps attribute)

H

hint() (sophios.apis.python.tool_builder.CommandLineTool method)

I

ignore_aliases() (sophios.input_output.NoAliasDumper method) import_python_file() (in module sophios.python_cwl_adapter) initial_workdir() (sophios.apis.python.tool_builder.CommandLineTool method) InitialWorkDirRequirement (class in sophios.apis.python.tool_builder) inline_javascript() (sophios.apis.python.tool_builder.CommandLineTool method) inline_subworkflow() (in module sophios.inlineing) inline_subworkflow_cwl() (in module sophios.inlineing) inline_subworkflow_wic_tag() (in module sophios.inlineing) inlineinput_constructor() (in module sophios.utils_yaml) InlineJavascriptRequirement (class in sophios.apis.python.tool_builder) inplace_update (sophios.apis.python.tool_builder.InplaceUpdateRequirement attribute) inplace_update() (sophios.apis.python.tool_builder.CommandLineTool method) InplaceUpdateRequirement (class in sophios.apis.python.tool_builder)

Input (in module sophios.apis.python.tool_builder) input_mapping (sophios.wic_types.EnvData attribute) Inputs (class in sophios.apis.python.tool_builder) inputs (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.workflow.Step attribute) (sophios.apis.python.workflow.Workflow attribute) inputs_file_workflow (sophios.wic_types.EnvData attribute) inputs_workflow (sophios.wic_types.NodeData attribute) InputSpec (class in sophios.apis.python.tool_builder) insert_step_into_workflow() (in module sophios.compiler) intent() (sophios.apis.python.tool_builder.CommandLineTool method) is_valid_url() (in module sophios.utils) item_separator (sophios.apis.python.tool_builder.CommandLineBinding attribute) (sophios.apis.python.tool_builder.InputSpec attribute)

J

job_name (sophios.compute_payload.SlurmConfig attribute)

jobs (sophios.compute_payload.ComputeWorkflowPayload attribute)

L

label() (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) label_text (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) listing (sophios.apis.python.tool_builder.InitialWorkDirRequirement attribute) load_contents (sophios.apis.python.tool_builder.CommandOutputBinding attribute) load_contents() (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method)

load_contents_value (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) load_listing (sophios.apis.python.tool_builder.LoadListingRequirement attribute) load_listing() (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) load_listing_value (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) LoadListingRequirement (class in sophios.apis.python.tool_builder) log_level (sophios.compute_payload.ToilConfig attribute) logging_filters() (in module sophios.plugins)

M

main() (in module sophios.cwl_subinterpreter) (in module sophios.main) make_plugins_dag() (in module sophios.utils_graphs) make_tool_dag() (in module sophios.utils_graphs) maybe_add_requirements() (in module sophios.utils_cwl) memory (sophios.compute_payload.SlurmConfig attribute) merge_yml_trees() (in module sophios.ast) mode (sophios.compute_payload.OutputConfig attribute) module sophios.apis.python.tool_builder sophios.apis.python.workflow sophios.ast sophios.cli sophios.compiler sophios.compute_payload sophios.compute_submit sophios.cwl_subinterpreter sophios.inference sophios.inlineing sophios.input_output sophios.main sophios.plugins sophios.python_cwl_adapter sophios.run_local sophios.run_local_async sophios.schemas.wic_schema sophios.utils sophios.utils_cwl sophios.utils_graphs sophios.utils_yaml sophios.wic_types

move_adapters_and_examples() (in module sophios.input_output) move_slash_last() (in module sophios.inlineing)

N

name (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) (sophios.wic_types.NodeData attribute) named() (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) named_empty_schema() (in module sophios.schemas.wic_schema) named_id_schema() (in module sophios.schemas.wic_schema) named_null_schema() (in module sophios.schemas.wic_schema) named_schema() (in module sophios.schemas.wic_schema)

namespace() (sophios.apis.python.tool_builder.CommandLineTool method) namespaces (sophios.wic_types.NodeData attribute) network_access (sophios.apis.python.tool_builder.NetworkAccess attribute) network_access() (sophios.apis.python.tool_builder.CommandLineTool method) NetworkAccess (class in sophios.apis.python.tool_builder) networkx (sophios.wic_types.GraphReps attribute) NoAliasDumper (class in sophios.input_output) NodeData (class in sophios.wic_types) nodes (sophios.compute_payload.SlurmConfig attribute) NoPartialFailureNullWarning (class in sophios.plugins) NoPreviouslyDefinedFilter (class in sophios.plugins) NoResolvedFilter (class in sophios.plugins)

O

outdir_max (sophios.apis.python.tool_builder.ResourceRequirement attribute) outdir_min (sophios.apis.python.tool_builder.ResourceRequirement attribute) Output (in module sophios.apis.python.tool_builder) output (sophios.compute_payload.ComputeConfig attribute) (sophios.compute_payload.SlurmConfig attribute) output_dir (sophios.compute_payload.OutputConfig attribute) output_eval (sophios.apis.python.tool_builder.CommandOutputBinding attribute) (sophios.apis.python.tool_builder.OutputSpec attribute)

output_mapping (sophios.wic_types.EnvData attribute) OutputConfig (class in sophios.compute_payload) Outputs (class in sophios.apis.python.tool_builder) outputs (sophios.apis.python.tool_builder.CommandLineTool attribute) (sophios.apis.python.workflow.Step attribute) (sophios.apis.python.workflow.Workflow attribute) OutputSpec (class in sophios.apis.python.tool_builder)

P

package (sophios.apis.python.tool_builder.SoftwarePackage attribute) packages (sophios.apis.python.tool_builder.SoftwareRequirement attribute) parse_int_string_tuple() (in module sophios.utils) parse_provenance_output_files() (in module sophios.utils) parse_provenance_output_files_() (in module sophios.utils) parse_step_name_str() (in module sophios.utils) partition (sophios.compute_payload.SlurmConfig attribute) partition_by_lowest_common_ancestor() (in module sophios.utils) path (sophios.apis.python.tool_builder.ValidationResult attribute) pattern (sophios.apis.python.tool_builder.SecondaryFile attribute)

perform_edge_inference() (in module sophios.inference) permanent_fail_codes() (sophios.apis.python.tool_builder.CommandLineTool method) plugin_ns (sophios.wic_types.StepId attribute) position (sophios.apis.python.tool_builder.CommandLineBinding attribute) (sophios.apis.python.tool_builder.InputSpec attribute) prefix (sophios.apis.python.tool_builder.CommandLineBinding attribute) pretty_print_forest() (in module sophios.utils) process (sophios.apis.python.tool_builder.ValidationResult attribute) process_name (sophios.apis.python.workflow.Step attribute) (sophios.apis.python.workflow.Workflow attribute) python_script_generate_cwl() (in module sophios.ast)

R

ram_max (sophios.apis.python.tool_builder.ResourceRequirement attribute) ram_min (sophios.apis.python.tool_builder.ResourceRequirement attribute) read_ast_from_disk() (in module sophios.ast) read_config_from_disk() (in module sophios.input_output) read_lines_pairs() (in module sophios.input_output) record() (sophios.apis.python.tool_builder.FieldSpec class method) (sophios.apis.python.tool_builder.InputSpec class method) (sophios.apis.python.tool_builder.OutputSpec class method) record_field() (in module sophios.apis.python.tool_builder) record_type() (in module sophios.apis.python.tool_builder) recursively_contains_dict_key() (in module sophios.utils) recursively_delete_dict_key() (in module sophios.utils) reindex_wic_steps() (in module sophios.utils) remove_entrypoints() (in module sophios.plugins) remove_entrypoints_docker() (in module sophios.plugins) remove_entrypoints_podman() (in module sophios.plugins) remove_id_tags() (in module sophios.utils_cwl)

require_step_id() (in module sophios.utils) require_string_out_keys() (in module sophios.utils_cwl) required (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) (sophios.apis.python.tool_builder.SecondaryFile attribute) requirement() (sophios.apis.python.tool_builder.CommandLineTool method) rerun_cwltool() (in module sophios.cwl_subinterpreter) ResourceRequirement (class in sophios.apis.python.tool_builder) resources() (sophios.apis.python.tool_builder.CommandLineTool method) restore_namespaced_output_name() (in module sophios.utils) rose (sophios.wic_types.CompilerInfo attribute) RoseTree (class in sophios.wic_types) run() (sophios.apis.python.workflow.Workflow method) run_compute() (in module sophios.run_local) run_cwl_serialized() (in module sophios.run_local_async) run_cwl_workflow() (in module sophios.run_local_async) run_local() (in module sophios.run_local) run_path (sophios.wic_types.Tool attribute)

S

sanitize_env_vars() (in module sophios.run_local) save() (sophios.apis.python.tool_builder.CommandLineTool method) scatter (sophios.apis.python.workflow.Step attribute) scatter_on() (sophios.apis.python.workflow.Step method) scatterMethod (sophios.apis.python.workflow.Step attribute) schema() (sophios.apis.python.tool_builder.CommandLineTool method) schema_definitions() (sophios.apis.python.tool_builder.CommandLineTool method) SchemaDefRequirement (class in sophios.apis.python.tool_builder) secondary_file() (in module sophios.apis.python.tool_builder) secondary_files() (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) secondary_files_value (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) SecondaryFile (class in sophios.apis.python.tool_builder) separate (sophios.apis.python.tool_builder.CommandLineBinding attribute) (sophios.apis.python.tool_builder.InputSpec attribute) service_default() (sophios.compute_payload.OutputConfig class method) shell_command() (sophios.apis.python.tool_builder.CommandLineTool method) shell_quote (sophios.apis.python.tool_builder.CommandLineBinding attribute) (sophios.apis.python.tool_builder.InputSpec attribute) ShellCommandRequirement (class in sophios.apis.python.tool_builder) shorten_namespaced_output_name() (in module sophios.utils) slurm (sophios.compute_payload.ComputeConfig attribute) slurm_job_gpu_count (sophios.compute_payload.SlurmConfig attribute) SlurmConfig (class in sophios.compute_payload) software() (sophios.apis.python.tool_builder.CommandLineTool method) SoftwarePackage (class in sophios.apis.python.tool_builder) SoftwareRequirement (class in sophios.apis.python.tool_builder) sophios.apis.python.tool_builder module sophios.apis.python.workflow module sophios.ast module sophios.cli module sophios.compiler module sophios.compute_payload module sophios.compute_submit module sophios.cwl_subinterpreter module sophios.inference module sophios.inlineing module

sophios.input_output module sophios.main module sophios.plugins module sophios.python_cwl_adapter module sophios.run_local module sophios.run_local_async module sophios.schemas.wic_schema module sophios.utils module sophios.utils_cwl module sophios.utils_graphs module sophios.utils_yaml module sophios.wic_types module specs (sophios.apis.python.tool_builder.SoftwarePackage attribute) stage() (sophios.apis.python.tool_builder.CommandLineTool method) stderr() (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.OutputSpec class method) stdin() (sophios.apis.python.tool_builder.CommandLineTool method) stdout() (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.OutputSpec class method) stem (sophios.wic_types.StepId attribute) Step (class in sophios.apis.python.workflow) step_from_command_line_tool() (in module sophios.apis.python.tool_builder) step_id (sophios.wic_types.YamlTree attribute) step_name_1 (sophios.wic_types.NodeData attribute) step_name_str() (in module sophios.utils) StepId (class in sophios.wic_types) steps (sophios.apis.python.workflow.Workflow attribute) streamable() (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) streamable_value (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) sub_forests (sophios.wic_types.YamlForest attribute) sub_trees (sophios.wic_types.RoseTree attribute) submit_compute_json() (in module sophios.compute_submit) submit_compute_payload() (in module sophios.compute_submit) success_codes() (sophios.apis.python.tool_builder.CommandLineTool method)

T

tasks_per_node (sophios.compute_payload.SlurmConfig attribute) temporary_env() (in module sophios.run_local) temporary_fail_codes() (sophios.apis.python.tool_builder.CommandLineTool method) time_limit (sophios.compute_payload.SlurmConfig attribute) time_limit() (sophios.apis.python.tool_builder.CommandLineTool method) timelimit (sophios.apis.python.tool_builder.ToolTimeLimit attribute) tmpdir_max (sophios.apis.python.tool_builder.ResourceRequirement attribute) tmpdir_min (sophios.apis.python.tool_builder.ResourceRequirement attribute) to_dict() (sophios.apis.python.tool_builder.CommandLineBinding method) (sophios.apis.python.tool_builder.CommandLineTool method) (sophios.apis.python.tool_builder.CommandOutputBinding method) (sophios.apis.python.tool_builder.Dirent method) (sophios.apis.python.tool_builder.EnvironmentDef method) (sophios.apis.python.tool_builder.FieldSpec method) (sophios.apis.python.tool_builder.InputSpec method) (sophios.apis.python.tool_builder.OutputSpec method) (sophios.apis.python.tool_builder.SecondaryFile method) (sophios.apis.python.tool_builder.SoftwarePackage method) (sophios.compute_payload.ComputeConfig method) (sophios.compute_payload.OutputConfig method) (sophios.compute_payload.SlurmConfig method) (sophios.compute_payload.ToilConfig method) to_fields() (sophios.apis.python.tool_builder.DockerRequirement method) (sophios.apis.python.tool_builder.EnvVarRequirement method) (sophios.apis.python.tool_builder.InitialWorkDirRequirement method) (sophios.apis.python.tool_builder.InlineJavascriptRequirement method) (sophios.apis.python.tool_builder.InplaceUpdateRequirement method) (sophios.apis.python.tool_builder.LoadListingRequirement method) (sophios.apis.python.tool_builder.NetworkAccess method) (sophios.apis.python.tool_builder.ResourceRequirement method) (sophios.apis.python.tool_builder.SchemaDefRequirement method) (sophios.apis.python.tool_builder.ShellCommandRequirement method) (sophios.apis.python.tool_builder.SoftwareRequirement method) (sophios.apis.python.tool_builder.ToolTimeLimit method) (sophios.apis.python.tool_builder.WorkReuse method)

to_step() (sophios.apis.python.tool_builder.CommandLineTool method) to_wic() (sophios.apis.python.workflow.Workflow method) to_yaml() (sophios.apis.python.tool_builder.CommandArgument method) (sophios.apis.python.tool_builder.CommandLineTool method) toil (sophios.compute_payload.ComputeConfig attribute) ToilConfig (class in sophios.compute_payload) Tool (class in sophios.wic_types) tool (sophios.wic_types.NodeData attribute) ToolBuilderValidationError ToolTimeLimit (class in sophios.apis.python.tool_builder) tree_to_forest() (in module sophios.ast) type_ (sophios.apis.python.tool_builder.FieldSpec attribute) (sophios.apis.python.tool_builder.InputSpec attribute) (sophios.apis.python.tool_builder.OutputSpec attribute) types (sophios.apis.python.tool_builder.SchemaDefRequirement attribute) types_match() (in module sophios.inference)

U

uri (sophios.apis.python.tool_builder.ValidationResult attribute)

user_specified() (sophios.compute_payload.OutputConfig class method)

V

validate() (sophios.apis.python.tool_builder.CommandLineTool method) validate_compute_payload() (in module sophios.compute_payload) validate_cwl() (in module sophios.plugins) validate_cwl_document() (in module sophios.apis.python.tool_builder) validate_out_tag() (in module sophios.utils_cwl)

ValidationResult (class in sophios.apis.python.tool_builder) value (sophios.apis.python.tool_builder.CommandArgument attribute) value_from (sophios.apis.python.tool_builder.CommandLineBinding attribute) value_from() (sophios.apis.python.tool_builder.InputSpec method) vars_workflow_output_internal (sophios.wic_types.EnvData attribute) version (sophios.apis.python.tool_builder.SoftwarePackage attribute)

W

when (sophios.apis.python.workflow.Step attribute) wic_loader() (in module sophios.utils_yaml) wic_main_schema() (in module sophios.schemas.wic_schema) wic_tag_schema() (in module sophios.schemas.wic_schema) work_reuse() (sophios.apis.python.tool_builder.CommandLineTool method) Workflow (class in sophios.apis.python.workflow) workflow_declared() (sophios.compute_payload.OutputConfig class method) workflow_id (sophios.compute_payload.ComputeWorkflowPayload attribute)

workflow_inputs_file (sophios.wic_types.NodeData attribute) WorkReuse (class in sophios.apis.python.tool_builder) writable (sophios.apis.python.tool_builder.Dirent attribute) write_absolute_yaml_tags() (in module sophios.input_output) write_artifacts() (sophios.apis.python.workflow.Workflow method) write_ast_to_disk() (sophios.apis.python.workflow.Workflow method) write_config_to_disk() (in module sophios.input_output) write_to_disk() (in module sophios.input_output) write_wic() (sophios.apis.python.workflow.Workflow method)

Y

yaml (sophios.apis.python.workflow.Step attribute) (sophios.apis.python.workflow.Workflow property) yaml_tree (sophios.wic_types.YamlForest attribute) YamlForest (class in sophios.wic_types)

YamlTree (class in sophios.wic_types) yml (sophios.wic_types.NodeData attribute) (sophios.wic_types.YamlTree attribute) yml_path (sophios.apis.python.workflow.Workflow attribute)