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.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) create_template_directories() (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 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) resolve_templates() (in module pype.misc) 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)
