Index Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | Q | R | S | T | U | V | W | Z Symbols --assume-yes nipoppy-pipeline-install command line option nipoppy-pipeline-upload command line option --bids-source nipoppy-init command line option --check-dicoms nipoppy-reorg command line option --community nipoppy-pipeline-search command line option --copy-files nipoppy-reorg command line option --dataset nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-install command line option nipoppy-pipeline-list command line option nipoppy-process command line option nipoppy-reorg command line option nipoppy-status command line option nipoppy-track-curation command line option nipoppy-track-processing command line option --dry-run nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-create command line option nipoppy-pipeline-install command line option nipoppy-pipeline-list command line option nipoppy-pipeline-search command line option nipoppy-pipeline-upload command line option nipoppy-pipeline-validate command line option nipoppy-process command line option nipoppy-reorg command line option nipoppy-status command line option nipoppy-track-curation command line option nipoppy-track-processing command line option --empty nipoppy-track-curation command line option --force nipoppy-init command line option nipoppy-pipeline-install command line option nipoppy-pipeline-upload command line option nipoppy-track-curation command line option --hpc nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option --keep-workdir nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option --layout nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-install command line option nipoppy-pipeline-list command line option nipoppy-process command line option nipoppy-reorg command line option nipoppy-status command line option nipoppy-track-curation command line option nipoppy-track-processing command line option --mode nipoppy-init command line option --n-jobs nipoppy-track-processing command line option --overwrite nipoppy-pipeline-install command line option --participant-id nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option nipoppy-track-processing command line option --password-file nipoppy-pipeline-install command line option nipoppy-pipeline-search command line option nipoppy-pipeline-upload command line option --pipeline nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option nipoppy-track-processing command line option --pipeline-step nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option nipoppy-track-processing command line option --pipeline-version nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option nipoppy-track-processing command line option --regenerate nipoppy-track-curation command line option --sandbox nipoppy-pipeline-install command line option nipoppy-pipeline-search command line option nipoppy-pipeline-upload command line option --session-id nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option nipoppy-track-processing command line option --simulate nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option --size nipoppy-pipeline-search command line option --source-descriptor nipoppy-pipeline-create command line option --tar nipoppy-process command line option --type nipoppy-pipeline-create command line option --use-subcohort nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option --verbose nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-create command line option nipoppy-pipeline-install command line option nipoppy-pipeline-list command line option nipoppy-pipeline-search command line option nipoppy-pipeline-upload command line option nipoppy-pipeline-validate command line option nipoppy-process command line option nipoppy-reorg command line option nipoppy-status command line option nipoppy-track-curation command line option nipoppy-track-processing command line option --version nipoppy command line option --write-subcohort nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-process command line option --yes nipoppy-pipeline-install command line option nipoppy-pipeline-upload command line option --zenodo-id nipoppy-pipeline-upload command line option -f nipoppy-init command line option nipoppy-pipeline-install command line option nipoppy-pipeline-upload command line option nipoppy-track-curation command line option -n nipoppy-pipeline-search command line option -s nipoppy-pipeline-search command line option -t nipoppy-pipeline-create command line option -v nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-create command line option nipoppy-pipeline-install command line option nipoppy-pipeline-list command line option nipoppy-pipeline-search command line option nipoppy-pipeline-upload command line option nipoppy-pipeline-validate command line option nipoppy-process command line option nipoppy-reorg command line option nipoppy-status command line option nipoppy-track-curation command line option nipoppy-track-processing command line option -y nipoppy-pipeline-install command line option nipoppy-pipeline-upload command line option A add_bind_arg() (nipoppy.container.BareMetalHandler method) (nipoppy.container.ContainerHandler method) add_env_arg() (nipoppy.container.BareMetalHandler method) (nipoppy.container.ContainerHandler method) add_file_handler() (nipoppy.logger.NipoppyLogger method) add_or_update_records() (nipoppy.tabular.base.BaseTabular method) add_path_suffix() (in module nipoppy.utils.utils) add_path_timestamp() (in module nipoppy.utils.utils) add_pybids_ignore_patterns() (in module nipoppy.utils.bids) alias_map (nipoppy.cli.groups.OrderedAliasedGroup attribute) ANALYSIS_LEVEL (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) API api_endpoint (nipoppy.zenodo_api.ZenodoAPI attribute) apply_analysis_level() (nipoppy.workflows.pipeline.BasePipelineWorkflow static method) (nipoppy.workflows.tracker.PipelineTracker static method) apply_fname_mapping() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) apply_pipeline_variables() (nipoppy.config.main.Config method) apply_substitutions_to_json() (in module nipoppy.utils.utils) Apptainer APPTAINER (nipoppy.env.ContainerCommandEnum attribute) ARGS (nipoppy.config.container.ContainerConfig attribute) args (nipoppy.container.ContainerHandler attribute) assume_yes (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow attribute) assume_yes_option() (in module nipoppy.cli.options) B BIDS bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) BIDS_SESSION_PREFIX (in module nipoppy.env) bids_source (nipoppy.workflows.dataset_init.InitWorkflow attribute) BIDS_SUBJECT_PREFIX (in module nipoppy.env) BIDSIFICATION (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) bind_flags (nipoppy.container.ApptainerHandler attribute) (nipoppy.container.BareMetalHandler attribute) (nipoppy.container.ContainerHandler property) (nipoppy.container.DockerHandler attribute) BIND_PATHS (nipoppy.config.container.ContainerConfig attribute) BIND_SEP (in module nipoppy.container) bosh_runner (nipoppy.workflows.runner.Runner property) Boutiques boutiques_config (nipoppy.workflows.pipeline.BasePipelineWorkflow property) BOUTIQUES_CONFIG_KEY (in module nipoppy.config.boutiques) BOUTIQUES_CUSTOM_KEY (in module nipoppy.config.boutiques) BUG_REPORT_URL (in module nipoppy.cli) (in module nipoppy.env) C check_command_exists() (nipoppy.container.ContainerHandler method) check_dicoms (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) check_input() (nipoppy.config.main.Config class method) check_participant_id() (in module nipoppy.utils.bids) check_pipeline_bundle() (in module nipoppy.pipeline_validation) check_pipeline_step() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_pipeline_version() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_session_id() (in module nipoppy.utils.bids) check_status() (nipoppy.tabular.processing_status.ProcessingStatusModel class method) (nipoppy.workflows.tracker.PipelineTracker method) CLI client (nipoppy.zenodo_api.ZenodoAPI attribute) close() (nipoppy.zenodo_api.ZenodoAPI method) code (nipoppy.cli.NipoppyError attribute) (nipoppy.exceptions.ConfigError attribute) (nipoppy.exceptions.ContainerError attribute) (nipoppy.exceptions.ExecutionError attribute) (nipoppy.exceptions.JSONError attribute) (nipoppy.exceptions.LayoutError attribute) (nipoppy.exceptions.NipoppyError attribute) (nipoppy.exceptions.TabularError attribute) (nipoppy.exceptions.TerminatedByUserError attribute) (nipoppy.exceptions.WorkflowError attribute) col_bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_community (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) col_datatype (nipoppy.tabular.manifest.Manifest attribute) col_description (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) col_downloads (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) col_in_bids (nipoppy.tabular.curation_status.CurationStatusTable attribute) col_in_post_reorg (nipoppy.tabular.curation_status.CurationStatusTable attribute) col_in_pre_reorg (nipoppy.tabular.curation_status.CurationStatusTable attribute) col_participant_dicom_dir (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) col_participant_id (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_pipeline (nipoppy.workflows.dataset_status.StatusWorkflow attribute) col_pipeline_name (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_pipeline_step (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_pipeline_version (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_session_id (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_status (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_title (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) col_visit_id (nipoppy.tabular.manifest.Manifest attribute) col_zenodo_id (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) COMMAND (nipoppy.config.container.ContainerConfig attribute) command (nipoppy.container.ApptainerHandler attribute) (nipoppy.container.BareMetalHandler attribute) (nipoppy.container.ContainerHandler property) (nipoppy.container.DockerHandler attribute) (nipoppy.container.SingularityHandler attribute) COMMON_HTML_TAGS (in module nipoppy.utils.html) community (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) concatenate() (nipoppy.tabular.base.BaseTabular method) conda config (nipoppy.layout.DatasetLayout attribute) (nipoppy.study.Study property) CONSOLE_FORMAT (in module nipoppy.logger) CONSOLE_STDERR (in module nipoppy.console) CONSOLE_STDOUT (in module nipoppy.console) CONTAINER_CONFIG CONTAINER_ERROR (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) CONTAINER_INFO (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) copy() (in module nipoppy.utils.fileops) copy_files (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) copy_template() (in module nipoppy.workflows.dataset_init) create_bids_db() (in module nipoppy.utils.bids) create_bundle() (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow method) Curation status file curation_status_table (nipoppy.study.Study property) (nipoppy.workflows.base.BaseDatasetWorkflow property) CURRENT_CONSOLE_WIDTH (in module nipoppy.workflows.pipeline_store.search) CURRENT_SCHEMA_VERSION (in module nipoppy.env) CUSTOM (nipoppy.config.main.Config attribute) D dataset_option() (in module nipoppy.cli.options) datatype (nipoppy.tabular.manifest.ManifestModel attribute) DATE_FORMAT (in module nipoppy.logger) DEFAULT_DOTENV_PATHS (in module nipoppy.env) default_hint (nipoppy.cli.NipoppyError attribute) (nipoppy.exceptions.ConfigError attribute) (nipoppy.exceptions.ContainerError attribute) (nipoppy.exceptions.ExecutionError attribute) (nipoppy.exceptions.FileOperationError attribute) (nipoppy.exceptions.JSONError attribute) (nipoppy.exceptions.LayoutError attribute) (nipoppy.exceptions.NipoppyError attribute) (nipoppy.exceptions.TabularError attribute) (nipoppy.exceptions.WorkflowError attribute) DEFAULT_LAYOUT_INFO (in module nipoppy.layout) DEFAULT_PIPELINE_STEP_NAME (in module nipoppy.env) dep_params() (in module nipoppy.cli.options) DESCRIPTION (nipoppy.config.pipeline.BasePipelineConfig attribute) description (nipoppy.layout.PathInfo attribute) descriptor (nipoppy.workflows.pipeline.BasePipelineWorkflow property) DESCRIPTOR_FILE (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) dicom_dir_map (nipoppy.workflows.base.BaseDatasetWorkflow property) DICOM_DIR_MAP_FILE (nipoppy.config.main.Config attribute) DICOM_DIR_PARTICIPANT_FIRST (nipoppy.config.main.Config attribute) DISCORD_URL (in module nipoppy.cli) (in module nipoppy.env) dname_hpc_logs (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) dname_pipeline_idp (nipoppy.layout.DatasetLayout attribute) dname_pipeline_output (nipoppy.layout.DatasetLayout attribute) Docker DOCKER (nipoppy.env.ContainerCommandEnum attribute) download_record_files() (nipoppy.zenodo_api.ZenodoAPI method) dpath_assessments (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_bids (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_code (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_containers (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_DATA (in module nipoppy.utils.utils) dpath_derivatives (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_descriptions (nipoppy.layout.DatasetLayout property) dpath_downloads (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_EXAMPLES (in module nipoppy.utils.utils) DPATH_HPC (in module nipoppy.utils.utils) dpath_hpc (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_LAYOUTS (in module nipoppy.utils.utils) dpath_logs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_nipoppy (nipoppy.layout.DatasetLayout attribute) dpath_pipeline (nipoppy.workflows.bids_conversion.BIDSificationRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow attribute) (nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow attribute) dpath_pipeline_bids_db (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_bundle (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_idp (nipoppy.workflows.extractor.ExtractionRunner property) dpath_pipeline_output (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_work (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipelines (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_post_reorg (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pre_reorg (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pybids_db (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_root (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseDatasetWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) dpath_scratch (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_sourcedata (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_src_imaging (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_src_tabular (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_tabular (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_work (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpaths_to_check (nipoppy.workflows.bids_conversion.BIDSificationRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.processing_runner.ProcessingRunner property) dry_run (nipoppy.workflows.base.BaseWorkflow attribute) E EMPHASIZE (nipoppy.logger.LogColor attribute) emphasize() (in module nipoppy.logger) empty (nipoppy.workflows.track_curation.TrackCurationWorkflow attribute) env_flag (nipoppy.container.ContainerHandler attribute) ENV_VARS (nipoppy.config.container.ContainerConfig attribute) equals() (nipoppy.tabular.base.BaseTabular method) exception_handler() (in module nipoppy.cli) EXT_LOG (in module nipoppy.env) EXT_TAR (in module nipoppy.env) EXTRACTION (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) F FAILURE (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) (nipoppy.logger.LogColor attribute) failure() (nipoppy.logger.NipoppyLogger method) FAKE_SESSION_ID (in module nipoppy.env) fed (nipoppy.utils.html.SelectiveHTMLStripper attribute) FIELD_DESCRIPTION_MAP (in module nipoppy.utils.utils) FILE (nipoppy.config.container.ContainerInfo attribute) FILE_FORMAT (in module nipoppy.logger) find_duplicates() (nipoppy.tabular.base.BaseTabular method) fix_bind_args() (nipoppy.container.ContainerHandler method) fname_hpc_error (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) fname_job_script (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) fname_pipeline_config (nipoppy.layout.DatasetLayout attribute) fname_readme (nipoppy.workflows.dataset_init.InitWorkflow attribute) force (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow attribute) (nipoppy.workflows.track_curation.TrackCurationWorkflow attribute) fpath_bids_dataset_description (nipoppy.layout.LayoutConfig attribute) fpath_bidsignore (nipoppy.layout.LayoutConfig attribute) fpath_config (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_container (nipoppy.workflows.pipeline.BasePipelineWorkflow property) fpath_curation_status (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_DEFAULT_LAYOUT (in module nipoppy.utils.utils) fpath_demographics (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_harmonized (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_HPC_TEMPLATE (in module nipoppy.utils.utils) fpath_layout (nipoppy.workflows.base.BaseDatasetWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) fpath_manifest (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_processing_status (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_SAMPLE_BIDS_DATASET_DESCRIPTION (in module nipoppy.utils.utils) FPATH_SAMPLE_BIDSIGNORE (in module nipoppy.utils.utils) FPATH_SAMPLE_CONFIG (in module nipoppy.utils.utils) FPATH_SAMPLE_DICOM_DIR_MAP (in module nipoppy.utils.utils) FPATH_SAMPLE_MANIFEST (in module nipoppy.utils.utils) fpath_spec (nipoppy.layout.DatasetLayout attribute) G generate_cli_command() (nipoppy.workflows.services.hpc.HPCRunner method) generate_curation_status_table() (in module nipoppy.tabular.curation_status) generate_fpath_log() (nipoppy.workflows.base.BaseDatasetWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) GENERATE_PYBIDS_DATABASE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) get_all_phenotypes() (nipoppy.NipoppyDataRetriever method) get_bidsified_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) get_boutiques_config_from_descriptor() (in module nipoppy.config.boutiques) get_command() (nipoppy.cli.groups.OrderedAliasedGroup method) get_completed_participants_sessions() (nipoppy.tabular.processing_status.ProcessingStatusTable method) get_container_handler() (in module nipoppy.container) get_data() (nipoppy.utils.html.SelectiveHTMLStripper method) get_derivatives() (nipoppy.NipoppyDataRetriever method) get_dicom_dir() (nipoppy.tabular.dicom_dir_map.DicomDirMap method) get_diff() (nipoppy.tabular.base.BaseTabular method) get_downloaded_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) get_dpath_pipeline() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_bundle() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_idp() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_output() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_store() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_work() (nipoppy.layout.DatasetLayout method) get_dpath_pybids_db() (nipoppy.layout.DatasetLayout method) get_fpaths_to_reorg() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) get_full_path() (nipoppy.layout.DatasetLayout method) get_imaging_subset() (nipoppy.tabular.manifest.Manifest method) get_latest_version_id() (nipoppy.zenodo_api.ZenodoAPI method) get_logger() (in module nipoppy.cli) (in module nipoppy.logger) get_organized_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) get_participants_sessions() (nipoppy.tabular.manifest.Manifest method) get_participants_sessions_to_run() (nipoppy.workflows.bids_conversion.BIDSificationRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.processing_runner.ProcessingRunner method) (nipoppy.workflows.tracker.PipelineTracker method) get_path_info() (nipoppy.layout.LayoutConfig method) get_paths() (nipoppy.layout.DatasetLayout method) get_phenotypes() (nipoppy.NipoppyDataRetriever method) get_pipeline_tag() (in module nipoppy.utils.utils) get_pipeline_version() (in module nipoppy.workflows.pipeline) get_pull_command() (nipoppy.container.ApptainerHandler method) (nipoppy.container.BareMetalHandler method) (nipoppy.container.ContainerHandler method) (nipoppy.container.DockerHandler method) get_pull_confirmation_prompt() (nipoppy.container.ApptainerHandler method) (nipoppy.container.BareMetalHandler method) (nipoppy.container.ContainerHandler method) (nipoppy.container.DockerHandler method) get_record_metadata() (nipoppy.zenodo_api.ZenodoAPI method) get_series_class() (nipoppy.tabular.base.BaseTabular method) get_shell_command() (nipoppy.container.ContainerHandler method) get_status() (nipoppy.tabular.curation_status.CurationStatusTable method) get_step_config() (nipoppy.config.pipeline.BasePipelineConfig method) get_tabular_data() (nipoppy.NipoppyDataRetriever method) get_today() (in module nipoppy.utils.utils) get_variables() (nipoppy.config.main.PipelineVariables method) Global config file global_options() (in module nipoppy.cli.options) group (nipoppy.config.pipeline_step.AnalysisLevelType attribute) H handle_bids_source() (nipoppy.workflows.dataset_init.InitWorkflow method) handle_data() (nipoppy.utils.html.SelectiveHTMLStripper method) handle_endtag() (nipoppy.utils.html.SelectiveHTMLStripper method) handle_startendtag() (nipoppy.utils.html.SelectiveHTMLStripper method) handle_starttag() (nipoppy.utils.html.SelectiveHTMLStripper method) HASH_LENGTH (in module nipoppy.workflows.dicom_reorg) hint (nipoppy.cli.NipoppyError attribute) (nipoppy.exceptions.NipoppyError attribute) HPC hpc (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) hpc_config (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.services.hpc.HPCRunner attribute) HPC_CONFIG_FILE (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) HPC_PREAMBLE (nipoppy.config.main.Config attribute) hpc_runner (nipoppy.workflows.runner.Runner property) I in_bids (nipoppy.tabular.curation_status.CurationStatusModel attribute) in_post_reorg (nipoppy.tabular.curation_status.CurationStatusModel attribute) in_pre_reorg (nipoppy.tabular.curation_status.CurationStatusModel attribute) index_cols (nipoppy.tabular.base.BaseTabular attribute) (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) INHERIT (nipoppy.config.container.ContainerConfig attribute) INVALID_COMMAND (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) INVALID_CONFIG (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) INVALID_LAYOUT (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) INVALID_TABULAR_DATA (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) invocation (nipoppy.workflows.pipeline.BasePipelineWorkflow property) INVOCATION_FILE (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) is_derived_dicom() (in module nipoppy.workflows.dicom_reorg) is_image_downloaded() (nipoppy.container.ApptainerHandler method) (nipoppy.container.BareMetalHandler method) (nipoppy.container.ContainerHandler method) (nipoppy.container.DockerHandler method) is_nipoppy_project() (in module nipoppy.utils.utils) J JOBLIB_INSTALLED (in module nipoppy.workflows.pipeline) JSON K keep_workdir (nipoppy.workflows.runner.Runner attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) KNOWN_FAILURE (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) L launch_boutiques_run() (nipoppy.workflows.runner.Runner method) layout (nipoppy.study.Study attribute) layout_option() (in module nipoppy.cli.options) list_commands() (nipoppy.cli.groups.OrderedAliasedGroup method) load() (nipoppy.config.main.Config class method) (nipoppy.tabular.base.BaseTabular class method) (nipoppy.tabular.manifest.Manifest class method) load_json() (in module nipoppy.utils.utils) load_or_generate() (nipoppy.tabular.dicom_dir_map.DicomDirMap class method) logger (in module nipoppy.cli) (in module nipoppy.cli.groups) (in module nipoppy.cli.options) (in module nipoppy.container) (in module nipoppy.pipeline_validation) (in module nipoppy.study) (in module nipoppy.tabular.base) (in module nipoppy.tabular.curation_status) (in module nipoppy.utils.fileops) (in module nipoppy.workflows.base) (in module nipoppy.workflows.dataset_init) (in module nipoppy.workflows.dataset_status) (in module nipoppy.workflows.dicom_reorg) (in module nipoppy.workflows.pipeline) (in module nipoppy.workflows.pipeline_store.create) (in module nipoppy.workflows.pipeline_store.install) (in module nipoppy.workflows.pipeline_store.list) (in module nipoppy.workflows.pipeline_store.search) (in module nipoppy.workflows.pipeline_store.upload) (in module nipoppy.workflows.pipeline_store.validate) (in module nipoppy.workflows.processing_runner) (in module nipoppy.workflows.runner) (in module nipoppy.workflows.services.boutiques) (in module nipoppy.workflows.services.hpc) (in module nipoppy.workflows.track_curation) (in module nipoppy.workflows.tracker) (nipoppy.zenodo_api.ZenodoAPI property) M make_context() (nipoppy.cli.groups.OrderedAliasedGroupWithDotenv method) manifest (nipoppy.study.Study property) Manifest file merge() (nipoppy.config.container.ContainerConfig method) message (nipoppy.cli.NipoppyError attribute) (nipoppy.exceptions.NipoppyError attribute) MINIMIZED_TABLE_MAX_WIDTH (in module nipoppy.workflows.pipeline_store.search) MISSING_DEPENDENCY (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) mkdir() (in module nipoppy.utils.fileops) mode (nipoppy.workflows.dataset_init.InitWorkflow attribute) model (nipoppy.tabular.base.BaseTabular property) (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) model_config (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.container.ContainerInfo attribute) (nipoppy.config.hpc.HpcConfig attribute) (nipoppy.config.main.Config attribute) (nipoppy.config.main.PipelineVariables attribute) (nipoppy.config.pipeline.BIDSificationPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline.ProcessingPipelineConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ExtractionPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.layout.LayoutConfig attribute) (nipoppy.tabular.manifest.ManifestModel attribute) module nipoppy nipoppy.base nipoppy.cli nipoppy.cli.groups nipoppy.cli.options nipoppy.cli.pipeline_catalog nipoppy.config nipoppy.config.boutiques nipoppy.config.container nipoppy.config.hpc nipoppy.config.main nipoppy.config.pipeline nipoppy.config.pipeline_step nipoppy.config.tracker nipoppy.console nipoppy.container nipoppy.env nipoppy.exceptions nipoppy.layout nipoppy.logger nipoppy.pipeline_validation nipoppy.study nipoppy.tabular nipoppy.tabular.base nipoppy.tabular.curation_status nipoppy.tabular.dicom_dir_map nipoppy.tabular.manifest nipoppy.tabular.processing_status nipoppy.utils nipoppy.utils.bids nipoppy.utils.fileops nipoppy.utils.html nipoppy.utils.utils nipoppy.workflows nipoppy.workflows.base nipoppy.workflows.bids_conversion nipoppy.workflows.dataset_init nipoppy.workflows.dataset_status nipoppy.workflows.dicom_reorg nipoppy.workflows.extractor nipoppy.workflows.pipeline nipoppy.workflows.pipeline_store nipoppy.workflows.pipeline_store.create nipoppy.workflows.pipeline_store.install nipoppy.workflows.pipeline_store.list nipoppy.workflows.pipeline_store.search nipoppy.workflows.pipeline_store.upload nipoppy.workflows.pipeline_store.validate nipoppy.workflows.processing_runner nipoppy.workflows.runner nipoppy.workflows.services nipoppy.workflows.services.boutiques nipoppy.workflows.services.hpc nipoppy.workflows.track_curation nipoppy.workflows.tracker nipoppy.zenodo_api movetree() (in module nipoppy.utils.fileops) MRI N n_jobs (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) n_success (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) n_total (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) NAME (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) (nipoppy.logger.NipoppyLogger attribute) name (nipoppy.workflows.base.BaseWorkflow attribute) nipoppy module nipoppy command line option --version nipoppy-bidsify command line option --dataset --dry-run --hpc --keep-workdir --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --simulate --use-subcohort --verbose --write-subcohort -v nipoppy-extract command line option --dataset --dry-run --hpc --keep-workdir --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --simulate --use-subcohort --verbose --write-subcohort -v nipoppy-init command line option --bids-source --dataset --dry-run --force --layout --mode --verbose -f -v nipoppy-pipeline-create command line option --dry-run --source-descriptor --type --verbose -t -v PIPELINE_DIR nipoppy-pipeline-install command line option --assume-yes --dataset --dry-run --force --layout --overwrite --password-file --sandbox --verbose --yes -f -v -y SOURCE nipoppy-pipeline-list command line option --dataset --dry-run --layout --verbose -v nipoppy-pipeline-search command line option --community --dry-run --password-file --sandbox --size --verbose -n -s -v QUERY nipoppy-pipeline-upload command line option --assume-yes --dry-run --force --password-file --sandbox --verbose --yes --zenodo-id -f -v -y PIPELINE_DIR nipoppy-pipeline-validate command line option --dry-run --verbose -v PATH nipoppy-process command line option --dataset --dry-run --hpc --keep-workdir --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --simulate --tar --use-subcohort --verbose --write-subcohort -v nipoppy-reorg command line option --check-dicoms --copy-files --dataset --dry-run --layout --verbose -v nipoppy-status command line option --dataset --dry-run --layout --verbose -v nipoppy-track-curation command line option --dataset --dry-run --empty --force --layout --regenerate --verbose -f -v nipoppy-track-processing command line option --dataset --dry-run --layout --n-jobs --participant-id --pipeline --pipeline-step --pipeline-version --session-id --verbose -v nipoppy.base module nipoppy.base.Base (built-in class) nipoppy.cli module nipoppy.cli.groups module nipoppy.cli.groups.OrderedAliasedGroup (built-in class) nipoppy.cli.groups.OrderedAliasedGroupWithDotenv (built-in class) nipoppy.cli.NipoppyError nipoppy.cli.options module nipoppy.cli.pipeline_catalog module nipoppy.cli.ReturnCode (built-in class) nipoppy.config module nipoppy.config.boutiques module nipoppy.config.boutiques.BoutiquesConfig (built-in class) nipoppy.config.container module nipoppy.config.container.ContainerConfig (built-in class) nipoppy.config.container.ContainerInfo (built-in class) nipoppy.config.hpc module nipoppy.config.hpc.HpcConfig (built-in class) nipoppy.config.main module nipoppy.config.main.Config (built-in class) nipoppy.config.main.PipelineVariables (built-in class) nipoppy.config.pipeline module nipoppy.config.pipeline.BasePipelineConfig (built-in class) nipoppy.config.pipeline.BIDSificationPipelineConfig (built-in class) nipoppy.config.pipeline.ExtractionPipelineConfig (built-in class) nipoppy.config.pipeline.PipelineInfo (built-in class) nipoppy.config.pipeline.ProcessingPipelineConfig (built-in class) nipoppy.config.pipeline_step module nipoppy.config.pipeline_step.AnalysisLevelType (built-in class) nipoppy.config.pipeline_step.BasePipelineStepConfig (built-in class) nipoppy.config.pipeline_step.BidsPipelineStepConfig (built-in class) nipoppy.config.pipeline_step.ExtractionPipelineStepConfig (built-in class) nipoppy.config.pipeline_step.ProcPipelineStepConfig (built-in class) nipoppy.config.tracker module nipoppy.config.tracker.TrackerConfig (built-in class) nipoppy.console module nipoppy.container module nipoppy.container.ApptainerHandler (built-in class) nipoppy.container.BareMetalHandler (built-in class) nipoppy.container.ContainerHandler (built-in class) nipoppy.container.DockerHandler (built-in class) nipoppy.container.SingularityHandler (built-in class) nipoppy.env module nipoppy.env.ContainerCommandEnum (built-in class) nipoppy.env.PipelineTypeEnum (built-in class) nipoppy.exceptions module nipoppy.exceptions.ConfigError nipoppy.exceptions.ContainerError nipoppy.exceptions.ExecutionError nipoppy.exceptions.FileOperationError nipoppy.exceptions.JSONError nipoppy.exceptions.LayoutError nipoppy.exceptions.NipoppyError nipoppy.exceptions.ReturnCode (built-in class) nipoppy.exceptions.TabularError nipoppy.exceptions.TerminatedByUserError nipoppy.exceptions.WorkflowError nipoppy.layout module nipoppy.layout.DatasetLayout (built-in class) nipoppy.layout.DpathInfo (built-in class) nipoppy.layout.FpathInfo (built-in class) nipoppy.layout.LayoutConfig (built-in class) nipoppy.layout.OptionalDpathInfo (built-in class) nipoppy.layout.OptionalFpathInfo (built-in class) nipoppy.layout.PathInfo (built-in class) nipoppy.logger module nipoppy.logger.LogColor (built-in class) nipoppy.logger.NipoppyLogger (built-in class) nipoppy.NipoppyDataRetriever (built-in class) nipoppy.pipeline_validation module nipoppy.pipeline_validation.PipelineValidationError nipoppy.study module nipoppy.study.Study (built-in class) nipoppy.tabular module nipoppy.tabular.base module nipoppy.tabular.base.BaseTabular (built-in class) nipoppy.tabular.base.BaseTabularModel (built-in class) nipoppy.tabular.curation_status module nipoppy.tabular.curation_status.CurationStatusModel (built-in class) nipoppy.tabular.curation_status.CurationStatusTable (built-in class) nipoppy.tabular.dicom_dir_map module nipoppy.tabular.dicom_dir_map.DicomDirMap (built-in class) nipoppy.tabular.dicom_dir_map.DicomDirMapModel (built-in class) nipoppy.tabular.manifest module nipoppy.tabular.manifest.Manifest (built-in class) nipoppy.tabular.manifest.ManifestModel (built-in class) nipoppy.tabular.processing_status module nipoppy.tabular.processing_status.ProcessingStatusModel (built-in class) nipoppy.tabular.processing_status.ProcessingStatusTable (built-in class) nipoppy.utils module nipoppy.utils.bids module nipoppy.utils.fileops module nipoppy.utils.html module nipoppy.utils.html.SelectiveHTMLStripper (built-in class) nipoppy.utils.utils module nipoppy.workflows module nipoppy.workflows.base module nipoppy.workflows.base.BaseDatasetWorkflow (built-in class) nipoppy.workflows.base.BaseWorkflow (built-in class) nipoppy.workflows.base.CommandRunner (built-in class) nipoppy.workflows.base.LogPrefix (built-in class) nipoppy.workflows.bids_conversion module nipoppy.workflows.bids_conversion.BIDSificationRunner (built-in class) nipoppy.workflows.dataset_init module nipoppy.workflows.dataset_init.InitWorkflow (built-in class) nipoppy.workflows.dataset_status module nipoppy.workflows.dataset_status.StatusWorkflow (built-in class) nipoppy.workflows.dicom_reorg module nipoppy.workflows.dicom_reorg.DicomReorgWorkflow (built-in class) nipoppy.workflows.extractor module nipoppy.workflows.extractor.ExtractionRunner (built-in class) nipoppy.workflows.pipeline module nipoppy.workflows.pipeline.BasePipelineWorkflow (built-in class) nipoppy.workflows.pipeline_store module nipoppy.workflows.pipeline_store.create module nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow (built-in class) nipoppy.workflows.pipeline_store.install module nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow (built-in class) nipoppy.workflows.pipeline_store.list module nipoppy.workflows.pipeline_store.list.PipelineListWorkflow (built-in class) nipoppy.workflows.pipeline_store.search module nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow (built-in class) nipoppy.workflows.pipeline_store.upload module nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow (built-in class) nipoppy.workflows.pipeline_store.validate module nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow (built-in class) nipoppy.workflows.processing_runner module nipoppy.workflows.processing_runner.ProcessingRunner (built-in class) nipoppy.workflows.runner module nipoppy.workflows.runner.Runner (built-in class) nipoppy.workflows.services module nipoppy.workflows.services.boutiques module nipoppy.workflows.services.boutiques.BoshRunnerCallable (built-in class) nipoppy.workflows.services.boutiques.CommandBuilder (built-in class) nipoppy.workflows.services.boutiques.ErrorBuilder (built-in class) nipoppy.workflows.services.hpc module nipoppy.workflows.services.hpc.HPCRunner (built-in class) nipoppy.workflows.track_curation module nipoppy.workflows.track_curation.TrackCurationWorkflow (built-in class) nipoppy.workflows.tracker module nipoppy.workflows.tracker.PipelineTracker (built-in class) nipoppy.zenodo_api module nipoppy.zenodo_api.ChecksumError nipoppy.zenodo_api.ZenodoAPI (built-in class) nipoppy.zenodo_api.ZenodoAPIError NIPOPPY_DIR_NAME (in module nipoppy.env) NIPOPPY_ROOT (in module nipoppy.utils.utils) NO_PARTICIPANTS_OR_SESSIONS_TO_RUN (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) P PARTIAL_SUCCESS (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) (nipoppy.logger.LogColor attribute) participant (nipoppy.config.pipeline_step.AnalysisLevelType attribute) participant_dicom_dir (nipoppy.tabular.curation_status.CurationStatusModel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) participant_id (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) participant_id_to_bids_participant_id() (in module nipoppy.utils.bids) participant_session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) PARTICIPANT_SESSION_DIR (nipoppy.config.tracker.TrackerConfig attribute) password_file (nipoppy.zenodo_api.ZenodoAPI attribute) password_file_option() (in module nipoppy.cli.options) PATH nipoppy-pipeline-validate command line option path (nipoppy.layout.PathInfo attribute) path_infos (nipoppy.layout.LayoutConfig property) path_labels (nipoppy.layout.LayoutConfig property) PATHS (nipoppy.config.tracker.TrackerConfig attribute) pipeline() (in module nipoppy.cli.pipeline_catalog) pipeline_config (nipoppy.workflows.bids_conversion.BIDSificationRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) pipeline_create() (in module nipoppy.cli.pipeline_catalog) PIPELINE_DIR nipoppy-pipeline-create command line option nipoppy-pipeline-upload command line option pipeline_dir (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) PIPELINE_EXECUTION_ERROR (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) pipeline_install() (in module nipoppy.cli.pipeline_catalog) pipeline_list() (in module nipoppy.cli.pipeline_catalog) pipeline_name (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) pipeline_options() (in module nipoppy.cli.options) pipeline_search() (in module nipoppy.cli.pipeline_catalog) pipeline_step (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) pipeline_step_config (nipoppy.workflows.bids_conversion.BIDSificationRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PIPELINE_TYPE (nipoppy.config.pipeline.BasePipelineConfig attribute) PIPELINE_TYPE_TO_CLASS (in module nipoppy.pipeline_validation) pipeline_type_to_dname_map (nipoppy.layout.DatasetLayout attribute) pipeline_upload() (in module nipoppy.cli.pipeline_catalog) pipeline_validate() (in module nipoppy.cli.pipeline_catalog) PIPELINE_VARIABLES (nipoppy.config.main.Config attribute) pipeline_version (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) PROC_DEPENDENCIES (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) proc_pipeline_info (nipoppy.workflows.extractor.ExtractionRunner property) process_container_config() (nipoppy.workflows.runner.Runner method) process_template_json() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) process_template_str() (in module nipoppy.utils.utils) PROCESSING (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) Processing status file processing_status_table (nipoppy.study.Study property) (nipoppy.workflows.base.BaseDatasetWorkflow property) PROGRAM_NAME (in module nipoppy.env) progress_bar_description (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) (nipoppy.workflows.tracker.PipelineTracker attribute) propagate_container_config_to_pipeline() (nipoppy.config.main.Config method) PYBIDS_IGNORE_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) pybids_ignore_patterns (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PyPI Q QUERY nipoppy-pipeline-search command line option query (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) R record_id (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow attribute) RESIZED_CONSOLE_WIDTH (in module nipoppy.workflows.pipeline_store.search) return_code (nipoppy.workflows.base.BaseWorkflow attribute) rich_handler (in module nipoppy.logger) rm() (in module nipoppy.utils.fileops) RUN (nipoppy.workflows.base.LogPrefix attribute) run() (nipoppy.workflows.base.BaseWorkflow method) run_bosh_launch() (in module nipoppy.workflows.services.boutiques) run_bosh_simulate() (in module nipoppy.workflows.services.boutiques) run_cleanup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow method) (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow method) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow method) (nipoppy.workflows.processing_runner.ProcessingRunner method) run_main() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.bids_conversion.BIDSificationRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dataset_status.StatusWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow method) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow method) (nipoppy.workflows.pipeline_store.list.PipelineListWorkflow method) (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow method) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow method) (nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow method) (nipoppy.workflows.track_curation.TrackCurationWorkflow method) (nipoppy.workflows.tracker.PipelineTracker method) run_setup() (nipoppy.workflows.base.BaseDatasetWorkflow method) (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.processing_runner.ProcessingRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_single() (nipoppy.workflows.bids_conversion.BIDSificationRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.processing_runner.ProcessingRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_single_results (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) RUN_STDERR (nipoppy.workflows.base.LogPrefix attribute) RUN_STDOUT (nipoppy.workflows.base.LogPrefix attribute) runners_options() (in module nipoppy.cli.options) S sandbox (nipoppy.zenodo_api.ZenodoAPI attribute) save() (nipoppy.config.main.Config method) save_df_with_backup() (in module nipoppy.utils.utils) save_json() (in module nipoppy.utils.utils) save_with_backup() (nipoppy.tabular.base.BaseTabular method) SCHEMA_VERSION (nipoppy.config.pipeline.BasePipelineConfig attribute) search_records() (nipoppy.zenodo_api.ZenodoAPI method) sep (nipoppy.tabular.base.BaseTabular attribute) session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) Session ID session_id (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) session_id_to_bids_session_id() (in module nipoppy.utils.bids) session_ids (nipoppy.tabular.manifest.Manifest attribute) set_authorization() (nipoppy.zenodo_api.ZenodoAPI method) set_status() (nipoppy.tabular.curation_status.CurationStatusTable method) set_up_bids_db() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) set_variables() (nipoppy.config.main.PipelineVariables method) set_verbose() (nipoppy.logger.NipoppyLogger method) simulate (nipoppy.workflows.runner.Runner attribute) SINGULARITY (nipoppy.env.ContainerCommandEnum attribute) size (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) sort_values() (nipoppy.tabular.base.BaseTabular method) SOURCE nipoppy-pipeline-install command line option source (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) source_descriptor (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) status (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) status_cols (nipoppy.tabular.curation_status.CurationStatusTable attribute) STATUS_FAIL (in module nipoppy.tabular.processing_status) status_fail (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) STATUS_INCOMPLETE (in module nipoppy.tabular.processing_status) status_incomplete (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) STATUS_SUCCESS (in module nipoppy.tabular.processing_status) status_success (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) STATUS_UNAVAILABLE (in module nipoppy.tabular.processing_status) status_unavailable (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) STEP (nipoppy.config.pipeline.PipelineInfo attribute) STEPS (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.BIDSificationPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.ProcessingPipelineConfig attribute) strip_html_tags() (in module nipoppy.utils.html) strip_tags (nipoppy.utils.html.SelectiveHTMLStripper attribute) StrOrPathLike (in module nipoppy.env) study (nipoppy.workflows.base.BaseDatasetWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) subcommand (nipoppy.workflows.services.hpc.HPCRunner attribute) submit() (nipoppy.workflows.services.hpc.HPCRunner method) SUBSTITUTIONS (nipoppy.config.main.Config attribute) SUCCESS (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) (nipoppy.logger.LogColor attribute) success() (nipoppy.logger.NipoppyLogger method) symlink() (in module nipoppy.utils.fileops) T tar (nipoppy.workflows.processing_runner.ProcessingRunner attribute) tar_directory() (nipoppy.workflows.processing_runner.ProcessingRunner method) TEMPLATE_PIPELINE_PATH (in module nipoppy.utils.utils) TEMPLATE_REPLACE_PATTERN (in module nipoppy.utils.utils) TERMINATED (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) timeout (nipoppy.zenodo_api.ZenodoAPI attribute) Tracker config file tracker_config (nipoppy.workflows.pipeline.BasePipelineWorkflow property) TRACKER_CONFIG_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) troubleshooting_hint (nipoppy.cli.NipoppyError property) (nipoppy.exceptions.NipoppyError property) type_ (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) U UNKNOWN_FAILURE (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) update_curation_status_table() (in module nipoppy.tabular.curation_status) UPDATE_STATUS (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) upload_record() (nipoppy.zenodo_api.ZenodoAPI method) URI (nipoppy.config.container.ContainerInfo attribute) use_subcohort (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) V validate() (nipoppy.layout.DatasetLayout method) (nipoppy.tabular.base.BaseTabular method) (nipoppy.tabular.manifest.Manifest method) validate_after() (nipoppy.config.container.ContainerInfo method) (nipoppy.config.hpc.HpcConfig method) (nipoppy.config.main.PipelineVariables method) (nipoppy.config.pipeline.BasePipelineConfig method) (nipoppy.config.pipeline.ExtractionPipelineConfig method) (nipoppy.config.pipeline_step.BasePipelineStepConfig method) (nipoppy.config.pipeline_step.BidsPipelineStepConfig method) (nipoppy.config.tracker.TrackerConfig method) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel method) (nipoppy.tabular.manifest.ManifestModel method) (nipoppy.tabular.processing_status.ProcessingStatusModel method) validate_and_process() (nipoppy.config.main.Config method) validate_before() (nipoppy.config.pipeline.BasePipelineConfig class method) (nipoppy.config.pipeline_step.BasePipelineStepConfig class method) (nipoppy.tabular.base.BaseTabularModel class method) (nipoppy.tabular.processing_status.ProcessingStatusModel class method) VARIABLES (nipoppy.config.pipeline.BasePipelineConfig attribute) venv verbose (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.services.hpc.HPCRunner attribute) VERSION (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) Visit ID visit_id (nipoppy.tabular.manifest.ManifestModel attribute) visit_ids (nipoppy.tabular.manifest.Manifest attribute) W WARNING (nipoppy.logger.LogColor attribute) warning() (nipoppy.logger.NipoppyLogger method) widths (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) WORKFLOW_FAILURE (nipoppy.cli.ReturnCode attribute) (nipoppy.exceptions.ReturnCode attribute) write_subcohort (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) Z zenodo_api (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow attribute) (nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow attribute) ZENODO_COMMUNITY_ID (in module nipoppy.env) zenodo_id (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) zenodo_options() (in module nipoppy.cli.pipeline_catalog)