Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | V | W | X _ __init__() (pype.exceptions.ArgumentError method) (pype.exceptions.BatchArgumentError method) (pype.exceptions.CommandError method) (pype.exceptions.EnvModulesError method) (pype.exceptions.InvalidTemplateVariableMixError method) (pype.exceptions.PipelineDependencyError method) (pype.exceptions.PipelineError method) (pype.exceptions.PipelineItemError method) (pype.exceptions.PipelineVersionError method) (pype.exceptions.ProfileError method) (pype.exceptions.PypeError method) (pype.exceptions.SnippetError method) (pype.exceptions.SnippetExecutionError method) (pype.exceptions.SnippetNotFoundError method) (pype.exceptions.SnippetResultsArgumentError method) (pype.exceptions.SnippetResultsTemplateSobstitutionError method) (pype.logger.ExtLog method) (pype.logger.PypeLogger method) (pype.misc.Tee method) (pype.process.Command method) (pype.process.DockerConfig method) (pype.process.Namespace method) (pype.process.Volume method) (pype.utils.pipeline.Pipeline method), [1] (pype.utils.pipeline.PipelineItem method), [1] A About add_input() (pype.process.Command method) add_log() (pype.logger.PypeLogger method) add_namespace() (pype.process.Command method) add_output() (pype.process.Command method) add_volume() (pype.process.Command method) ArgumentError B basename_no_extension() (in module pype.misc) bases_format() (in module pype.misc) Batch List Arguments BatchArgumentError bind_prefix (pype.process.Volume attribute), [1] bio-pype-builder Builder C cache_dir (pype.process.DockerConfig attribute), [1] capture_stdout() (pype.process.Command method) Carbon tracking CATEGORIES (pype.misc.SubcommandHelpFormatter attribute) check_exit_code() (in module pype.misc) child_close() (pype.process.Command method) close() (pype.process.Command method) cmd (pype.process.Command attribute) CO2eq Command (class in pype.process) CommandError CommandNamespaceError Composite Arguments conda_run() (pype.process.Command method) Configuration create_minimal_profile() (in module pype.misc) D DefaultHelpParser (class in pype.misc) docker (pype.process.Command attribute) docker_run() (pype.process.Command method) DockerConfig (class in pype.process) Dynamic Batch Expansion E Energy EnvModulesError error() (pype.misc.DefaultHelpParser method) exec_path (pype.process.DockerConfig attribute), [1] ExtLog (class in pype.logger) F first() (pype.process.Namespace method) G generate_batch_id() (pype.utils.pipeline.PipelineItem method) generate_uid() (in module pype.misc) Get started get_module_cmd() (in module pype.process) get_module_method() (in module pype.misc) get_modules() (in module pype.misc) get_modules_names() (in module pype.misc) get_pipelines() (in module pype.utils.pipeline) get_visible_pipelines() (in module pype.utils.pipeline) H has_same_basedir() (in module pype.process) human_format() (in module pype.misc) I import_module() (in module pype.misc) inputs (pype.process.Command attribute) InvalidTemplateVariableMixError is_direct_child_of() (in module pype.process) is_singularity (pype.process.DockerConfig property) is_udocker (pype.process.DockerConfig property) L last() (pype.process.Namespace method) local_run() (pype.process.Command method) log (pype.process.Command attribute) Logs LSP M module pype.exceptions pype.logger pype.misc pype.process pype.utils module_load() (pype.process.Command method) module_run() (pype.process.Command method) N name (pype.process.Command attribute) Namespace (class in pype.process) normalize_volumes() (pype.process.Command method) O output (pype.process.Volume attribute), [1] outputs (pype.process.Command attribute) P package_files() (in module pype.misc) package_modules() (in module pype.misc) path (pype.process.Volume attribute), [1] pipe_in() (pype.process.Command method) Pipeline (class in pype.utils.pipeline) Pipeline Builder Pipeline Resume PipelineDependencyError PipelineError PipelineItem (class in pype.utils.pipeline) PipelineItemError Pipelines PipelineVersionError profile (pype.process.Command attribute) ProfileError Profiles program_string() (in module pype.process) Progress Tracking pype.exceptions module pype.logger module pype.misc module pype.process module pype.utils module PYPE_CARBON_COUNTRY PYPE_CO2EQ_SRC PYPE_OVERLAY_MODE PypeError PypeLogger (class in pype.logger) Q Queue Systems R Registry release_stdout() (pype.process.Command method) remove_mode() (pype.process.Volume method) replace_bind_dirname() (pype.process.Volume method) replace_bind_volume() (pype.process.Volume method) replace_values_in_code() (pype.process.Command method) responsive_sleep() (in module pype.misc) Results Pattern Run run() (pype.process.Command method) (pype.utils.pipeline.PipelineItem method) runtime (pype.process.DockerConfig attribute), [1] S singularity_volume() (pype.process.Volume method) Snippet Outputs SnippetError SnippetExecutionError SnippetNotFoundError SnippetResultsArgumentError SnippetResultsTemplateSobstitutionError Snippets Split-Process-Merge Storage Backends StorageBackend SubcommandHelpFormatter (class in pype.misc) submit() (pype.utils.pipeline.Pipeline method) T Tee (class in pype.misc) Template-based Pipelines to_str() (pype.process.Volume method) try_import() (in module pype.misc) V Validation Volume (class in pype.process) volumes (pype.process.Command attribute) W Workflow Registry write() (pype.misc.Tee method) X xopen() (in module pype.misc)
