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‎man/.get_context.1

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.TH .GET_CONTEXT 1 2025-Jan "" "get current workflow environment context"
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.TH .GET_CONTEXT 1 2025-Feb "" "get current workflow environment context"
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.SH NAME
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.get_context \- .get_context()
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.SH SYNOPSIS

‎man/.internal_call.1

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.TH .INTERNAL_CALL 1 2025-Jan "" "Invoke an analysis application"
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.TH .INTERNAL_CALL 1 2025-Feb "" "Invoke an analysis application"
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.SH NAME
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.internal_call \- .internal_call(app, context)
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.SH SYNOPSIS

‎man/.onLoad.1

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.TH .ONLOAD 1 2025-Jan "" ".onLoad"
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.TH .ONLOAD 1 2025-Feb "" ".onLoad"
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.SH NAME
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.onLoad \- .onLoad()
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.SH SYNOPSIS

‎man/__build_app.1

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.TH __BUILD_APP 1 2025-Jan "" "Build workflow app object"
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.TH __BUILD_APP 1 2025-Feb "" "Build workflow app object"
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.SH NAME
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__build_app \- __build_app(f)
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.SH SYNOPSIS

‎man/__runImpl.1

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.TH __RUNIMPL 1 2025-Jan "" "An internal function for start the workflow"
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.TH __RUNIMPL 1 2025-Feb "" "An internal function for start the workflow"
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.SH NAME
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__runImpl \- __runImpl(context,
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<i>disables</i> = 'list'())

‎man/__workfile_uri_parser.1

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.TH __WORKFILE_URI_PARSER 1 2025-Jan "" "parse the workfile expression"
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.TH __WORKFILE_URI_PARSER 1 2025-Feb "" "parse the workfile expression"
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.SH NAME
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__workfile_uri_parser \- __workfile_uri_parser(uri)
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.SH SYNOPSIS

‎man/__workfiles.1

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.TH __WORKFILES 1 2025-Jan "" "parse the workfile expression"
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.TH __WORKFILES 1 2025-Feb "" "parse the workfile expression"
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.SH NAME
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__workfiles \- __workfiles(files.uri)
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.SH SYNOPSIS

‎man/app.1

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.TH APP 1 2025-Jan "" "Analysis app constructor"
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.TH APP 1 2025-Feb "" "Analysis app constructor"
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.SH NAME
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app \- app(name, analysis,
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<i>desc</i> = <span style='color: brown;'><strong>'no description'</strong></span>,

‎man/app_check.delegate.1

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.TH APP_CHECK.DELEGATE 1 2025-Jan "" "Check the function signature of the app function"
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.TH APP_CHECK.DELEGATE 1 2025-Feb "" "Check the function signature of the app function"
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.SH NAME
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app_check.delegate \- app_check.delegate(analysis)
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.SH SYNOPSIS

‎man/app_check.signature.1

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.TH APP_CHECK.SIGNATURE 1 2025-Jan "" "check of the required app slot"
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.TH APP_CHECK.SIGNATURE 1 2025-Feb "" "check of the required app slot"
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.SH NAME
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app_check.signature \- app_check.signature(app)
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.SH SYNOPSIS

‎man/check_dependency.1

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.TH CHECK_DEPENDENCY 1 2025-Jan "" "Check of the analysis app dependency"
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.TH CHECK_DEPENDENCY 1 2025-Feb "" "Check of the analysis app dependency"
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.SH NAME
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check_dependency \- check_dependency(app,
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<i>context</i> = '.get_context'())

‎man/check_dependency.context_env.1

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.TH CHECK_DEPENDENCY.CONTEXT_ENV 1 2025-Jan "" "Check of the required environment symbols"
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.TH CHECK_DEPENDENCY.CONTEXT_ENV 1 2025-Feb "" "Check of the required environment symbols"
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.SH NAME
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check_dependency.context_env \- check_dependency.context_env(requires, context)
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.SH SYNOPSIS

‎man/check_dependency.localfiles.1

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.TH CHECK_DEPENDENCY.LOCALFILES 1 2025-Jan "" "Check for the upstream file dependency"
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.TH CHECK_DEPENDENCY.LOCALFILES 1 2025-Feb "" "Check for the upstream file dependency"
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.SH NAME
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check_dependency.localfiles \- check_dependency.localfiles(requires, context)
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.SH SYNOPSIS

‎man/create_memory_context.1

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.TH CREATE_MEMORY_CONTEXT 1 2025-Jan "" "create an in-memory context object just used for run debug"
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.TH CREATE_MEMORY_CONTEXT 1 2025-Feb "" "create an in-memory context object just used for run debug"
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.SH NAME
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create_memory_context \- create_memory_context(
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<i>mounts</i> = <span style='color: blue !important;'>NULL</span>)

‎man/definePipeline.1

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.TH DEFINEPIPELINE 1 2025-Jan "" "Create a custom pipeline workflow execute sequence"
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.TH DEFINEPIPELINE 1 2025-Feb "" "Create a custom pipeline workflow execute sequence"
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.SH NAME
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definePipeline \- definePipeline(seq)
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.SH SYNOPSIS

‎man/dependency.context_env_missing.1

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.TH DEPENDENCY.CONTEXT_ENV_MISSING 1 2025-Jan "" "Generate the error message for missing context symbols"
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.TH DEPENDENCY.CONTEXT_ENV_MISSING 1 2025-Feb "" "Generate the error message for missing context symbols"
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.SH NAME
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dependency.context_env_missing \- dependency.context_env_missing(context)
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.SH SYNOPSIS

‎man/dependency.workfiles_missing.1

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.TH DEPENDENCY.WORKFILES_MISSING 1 2025-Jan "" "Generate the error message for the missing required work files"
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.TH DEPENDENCY.WORKFILES_MISSING 1 2025-Feb "" "Generate the error message for the missing required work files"
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.SH NAME
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dependency.workfiles_missing \- dependency.workfiles_missing(file)
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.SH SYNOPSIS

‎man/dependency_analysis.1

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.TH DEPENDENCY_ANALYSIS 1 2025-Jan "" "dependency_analysis"
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.TH DEPENDENCY_ANALYSIS 1 2025-Feb "" "dependency_analysis"
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.SH NAME
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dependency_analysis \- dependency_analysis(app)
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.SH SYNOPSIS

‎man/dependency_graph.1

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.TH DEPENDENCY_GRAPH 1 2025-Jan "" "try to extract the dependency graph from the application modules"
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.TH DEPENDENCY_GRAPH 1 2025-Feb "" "try to extract the dependency graph from the application modules"
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.SH NAME
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dependency_graph \- dependency_graph(mounts)
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.SH SYNOPSIS

‎man/echo_warning.1

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.TH ECHO_WARNING 1 2025-Jan "" "print warning message on the screen and the log file"
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.TH ECHO_WARNING 1 2025-Feb "" "print warning message on the screen and the log file"
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.SH NAME
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echo_warning \- echo_warning(msg,
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<i>app</i> = <span style='color: blue !important;'>NULL</span>)

‎man/extract_workflow_vertex.1

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.TH EXTRACT_WORKFLOW_VERTEX 1 2025-Jan "" "extract_workflow_vertex"
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.TH EXTRACT_WORKFLOW_VERTEX 1 2025-Feb "" "extract_workflow_vertex"
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.SH NAME
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extract_workflow_vertex \- extract_workflow_vertex(meta)
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.SH SYNOPSIS

‎man/filepath_safe.1

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.TH FILEPATH_SAFE 1 2025-Jan "" "Create the file path safely"
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.TH FILEPATH_SAFE 1 2025-Feb "" "Create the file path safely"
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.SH NAME
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filepath_safe \- filepath_safe(dir, filename,
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<i>maxchars</i> = <span style='color: green;'>48</span>)

‎man/finalize.1

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.TH FINALIZE 1 2025-Jan "" "Mark end of the analysis workflow"
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.TH FINALIZE 1 2025-Feb "" "Mark end of the analysis workflow"
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.SH NAME
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finalize \- finalize()
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.SH SYNOPSIS

‎man/get_appName.func_reference.1

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.TH GET_APPNAME.FUNC_REFERENCE 1 2025-Jan "" "get app name from the analysis function as reference"
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.TH GET_APPNAME.FUNC_REFERENCE 1 2025-Feb "" "get app name from the analysis function as reference"
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.SH NAME
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get_appName.func_reference \- get_appName.func_reference(app)
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.SH SYNOPSIS

‎man/get_appName.obj.1

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.TH GET_APPNAME.OBJ 1 2025-Jan "" "Get app name from the generated analysis app module"
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.TH GET_APPNAME.OBJ 1 2025-Feb "" "Get app name from the generated analysis app module"
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.SH NAME
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get_appName.obj \- get_appName.obj(app)
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.SH SYNOPSIS

‎man/get_app_name.1

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.TH GET_APP_NAME 1 2025-Jan "" "Helper function for get app name"
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.TH GET_APP_NAME 1 2025-Feb "" "Helper function for get app name"
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.SH NAME
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get_app_name \- get_app_name(app)
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.SH SYNOPSIS

‎man/get_config.1

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.TH GET_CONFIG 1 2025-Jan "" "get user parameter value inside current workflow context environment"
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.TH GET_CONFIG 1 2025-Feb "" "get user parameter value inside current workflow context environment"
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.SH NAME
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get_config \- get_config(name,
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<i>default</i> = <span style='color: blue !important;'>NULL</span>,

‎man/get_functionName.1

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.TH GET_FUNCTIONNAME 1 2025-Jan "" "get function name"
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.TH GET_FUNCTIONNAME 1 2025-Feb "" "get function name"
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.SH NAME
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get_functionName \- get_functionName(f)
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.SH SYNOPSIS

‎man/get_timestamp.1

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.TH GET_TIMESTAMP 1 2025-Jan "" "get a character vector of current timespan"
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.TH GET_TIMESTAMP 1 2025-Feb "" "get a character vector of current timespan"
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.SH NAME
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get_timestamp \- get_timestamp()
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.SH SYNOPSIS

‎man/has_cachefile.1

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.TH HAS_CACHEFILE 1 2025-Jan "" "check the cache file is exists or not"
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.TH HAS_CACHEFILE 1 2025-Feb "" "check the cache file is exists or not"
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.SH NAME
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has_cachefile \- has_cachefile(filepath)
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.SH SYNOPSIS

‎man/hook.1

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.TH HOOK 1 2025-Jan "" "Add workflow app component into the registry"
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.TH HOOK 1 2025-Feb "" "Add workflow app component into the registry"
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.SH NAME
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hook \- hook(app)
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.SH SYNOPSIS

‎man/init_context.1

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.TH INIT_CONTEXT 1 2025-Jan "" "This function should be call at first"
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.TH INIT_CONTEXT 1 2025-Feb "" "This function should be call at first"
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.SH NAME
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init_context \- init_context(
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<i>outputdir</i> = <span style='color: brown;'><strong>'./'</strong></span>)

‎man/pull_configs.1

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.TH PULL_CONFIGS 1 2025-Jan "" "pull all configuration value from workflow registry"
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.TH PULL_CONFIGS 1 2025-Feb "" "pull all configuration value from workflow registry"
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.SH NAME
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pull_configs \- pull_configs()
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.SH SYNOPSIS

‎man/result_dir.1

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.TH RESULT_DIR 1 2025-Jan "" "get directory folder path for the analysis output result"
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.TH RESULT_DIR 1 2025-Feb "" "get directory folder path for the analysis output result"
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.SH NAME
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result_dir \- result_dir()
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.SH SYNOPSIS

‎man/run.1

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.TH RUN 1 2025-Jan "" "Call this function to start run workflow"
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.TH RUN 1 2025-Feb "" "Call this function to start run workflow"
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.SH NAME
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run \- run(
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<i>registry</i> = <span style='color: blue !important;'>NULL</span>,

‎man/set_config.1

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.TH SET_CONFIG 1 2025-Jan "" "Set user parameters to the workflow context"
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.TH SET_CONFIG 1 2025-Feb "" "Set user parameters to the workflow context"
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.SH NAME
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set_config \- set_config(
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<i>configs</i> = 'list'())

‎man/set_dependency.1

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.TH SET_DEPENDENCY 1 2025-Jan "" "function for create application dependency data"
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.TH SET_DEPENDENCY 1 2025-Feb "" "function for create application dependency data"
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.SH NAME
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set_dependency \- set_dependency(
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<i>context.env</i> = 'list'(),

‎man/set_disable.1

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.TH SET_DISABLE 1 2025-Jan "" "Set workflow application disable flag"
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.TH SET_DISABLE 1 2025-Feb "" "Set workflow application disable flag"
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.SH NAME
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set_disable \- set_disable(app,
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<i>flag</i> = <span style='color: blue !important;'>TRUE</span>)

‎man/summary.1

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.TH SUMMARY 1 2025-Jan "" "Inspect the workflow analysis modules"
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.TH SUMMARY 1 2025-Feb "" "Inspect the workflow analysis modules"
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.SH NAME
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summary \- summary()
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.SH SYNOPSIS

‎man/tabulate_workflow_summary.1

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.TH TABULATE_WORKFLOW_SUMMARY 1 2025-Jan "" "Extract the workflow analysis contents"
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.TH TABULATE_WORKFLOW_SUMMARY 1 2025-Feb "" "Extract the workflow analysis contents"
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.SH NAME
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tabulate_workflow_summary \- tabulate_workflow_summary(pool)
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.SH SYNOPSIS

‎man/throw_err.1

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.TH THROW_ERR 1 2025-Jan "" "echo error message on the screen and then crash the workflow"
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.TH THROW_ERR 1 2025-Feb "" "echo error message on the screen and then crash the workflow"
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.SH NAME
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throw_err \- throw_err(msg)
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.SH SYNOPSIS

‎man/use_cache.1

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.TH USE_CACHE 1 2025-Jan "" "Work with cache file"
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.TH USE_CACHE 1 2025-Feb "" "Work with cache file"
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.SH NAME
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use_cache \- use_cache(filepath, create)
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.SH SYNOPSIS

‎man/workdir_root.1

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.TH WORKDIR_ROOT 1 2025-Jan "" "Get workspace root directory"
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.TH WORKDIR_ROOT 1 2025-Feb "" "Get workspace root directory"
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.SH NAME
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workdir_root \- workdir_root()
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.SH SYNOPSIS

‎man/workfile.1

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.TH WORKFILE 1 2025-Jan "" "Construct of the file path inside an app workspace"
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.TH WORKFILE 1 2025-Feb "" "Construct of the file path inside an app workspace"
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.SH NAME
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workfile \- workfile(app,
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<i>relpath</i> = <span style='color: blue !important;'>NULL</span>)

‎man/workspace.1

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.TH WORKSPACE 1 2025-Jan "" "get app workspace location"
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.TH WORKSPACE 1 2025-Feb "" "get app workspace location"
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.SH NAME
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workspace \- workspace(app)
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.SH SYNOPSIS

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