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 --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-install 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-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 --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-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 --tar nipoppy-process command line option --verbose nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-install 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-list 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-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-install 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 -s nipoppy-pipeline-search command line option -v nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-pipeline-install 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 access_token (nipoppy.zenodo_api.ZenodoAPI attribute) add_bind_path() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) add_bind_path_to_args() (in module nipoppy.config.container) add_logfile() (in module nipoppy.logger) add_or_update_records() (nipoppy.tabular.base.BaseTabular method) add_path_suffix() (in module nipoppy.utils) add_path_timestamp() (in module nipoppy.utils) add_pybids_ignore_patterns() (in module nipoppy.utils) ANALYSIS_LEVEL (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) API api_endpoint (nipoppy.zenodo_api.ZenodoAPI attribute) apply_analysis_level() (in module nipoppy.workflows.pipeline) apply_fname_mapping() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) apply_pipeline_variables() (nipoppy.config.Config method) (nipoppy.config.main.Config method) apply_substitutions_to_json() (in module nipoppy.utils) APPTAINER (nipoppy.env.ContainerCommandEnum attribute) APPTAINER_BIND_FLAG (in module nipoppy.config.container) APPTAINER_BIND_SEP (in module nipoppy.config.container) APPTAINER_ENVVAR_PREFIXES (in module nipoppy.config.container) ARGS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) assume_yes (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow attribute) (nipoppy.workflows.PipelineInstallWorkflow attribute) B BIDS bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) BIDS_PIPELINES bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) BIDS_SESSION_PREFIX (in module nipoppy.env) bids_source (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) BIDS_SUBJECT_PREFIX (in module nipoppy.env) BIDSIFICATION (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) Boutiques boutiques_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) BOUTIQUES_CONFIG_KEY (in module nipoppy.config.boutiques) BOUTIQUES_CUSTOM_KEY (in module nipoppy.config.boutiques) C capture_warnings() (in module nipoppy.logger) check_container_args() (in module nipoppy.config.container) check_container_command() (in module nipoppy.config.container) check_dicoms (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) check_dir() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_input() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) check_participant_id() (in module nipoppy.utils) check_pipeline_bundle() (in module nipoppy.pipeline_validation) check_pipeline_step() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_pipeline_version() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_session_id() (in module nipoppy.utils) check_status() (nipoppy.tabular.processing_status.ProcessingStatusModel class method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.tracker.PipelineTracker method) CLI col_bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_datatype (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_in_bids (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.CurationStatusTable attribute) col_in_post_reorg (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.CurationStatusTable attribute) col_in_pre_reorg (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.CurationStatusTable attribute) col_participant_dicom_dir (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) col_participant_id (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_pipeline (nipoppy.workflows.dataset_status.StatusWorkflow attribute) (nipoppy.workflows.StatusWorkflow attribute) col_pipeline_name (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_pipeline_step (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_pipeline_version (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_session_id (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_status (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) col_visit_id (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) COMMAND (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) concatenate() (nipoppy.tabular.base.BaseTabular method) conda config (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseDatasetWorkflow property) (nipoppy.workflows.BaseDatasetWorkflow property) CONSOLE_STDERR (in module nipoppy.console) CONSOLE_STDOUT (in module nipoppy.console) CONTAINER_CONFIG CONTAINER_INFO (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) copy() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) copy_files (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) copytree() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) create_bids_db() (in module nipoppy.utils) create_bundle() (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow method) create_symlink() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) Curation status file curation_status_table (nipoppy.workflows.base.BaseDatasetWorkflow property) (nipoppy.workflows.BaseDatasetWorkflow property) CURRENT_SCHEMA_VERSION (in module nipoppy.env) CUSTOM (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) D DATASET_ARGUMENT 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 DATASET_NAME datatype (nipoppy.tabular.manifest.ManifestModel attribute) DATE_FORMAT (in module nipoppy.logger) DEFAULT_LAYOUT_INFO (in module nipoppy.layout) DEFAULT_PIPELINE_STEP_NAME (in module nipoppy.env) DESCRIPTION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) description (nipoppy.layout.PathInfo attribute) descriptor (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) DESCRIPTOR_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) dicom_dir_map (nipoppy.workflows.base.BaseDatasetWorkflow property) (nipoppy.workflows.BaseDatasetWorkflow property) DICOM_DIR_MAP_FILE (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) DICOM_DIR_PARTICIPANT_FIRST (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) dname_hpc_logs (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) dname_pipeline_idp (nipoppy.layout.DatasetLayout attribute) dname_pipeline_output (nipoppy.layout.DatasetLayout 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) 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) DPATH_HPC (in module nipoppy.utils) dpath_hpc (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_LAYOUTS (in module nipoppy.utils) dpath_logs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_nipoppy (nipoppy.layout.DatasetLayout attribute) dpath_pipeline (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow attribute) (nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow attribute) (nipoppy.workflows.PipelineInstallWorkflow attribute) (nipoppy.workflows.PipelineValidateWorkflow attribute) dpath_pipeline_bids_db (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_bundle (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_idp (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) dpath_pipeline_output (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_work (nipoppy.workflows.BasePipelineWorkflow property) (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.BaseDatasetWorkflow 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.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.PipelineRunner property) (nipoppy.workflows.runner.PipelineRunner property) dry_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) E empty (nipoppy.workflows.track_curation.TrackCurationWorkflow attribute) (nipoppy.workflows.TrackCurationWorkflow attribute) ENV_VARS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) equals() (nipoppy.tabular.base.BaseTabular method) 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.env.LogColor attribute) FAKE_SESSION_ID (in module nipoppy.env) FIELD_DESCRIPTION_MAP (in module nipoppy.utils) FILE (nipoppy.config.container.ContainerInfo attribute) find_duplicates() (nipoppy.tabular.base.BaseTabular method) fname_hpc_error (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) fname_job_script (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) fname_pipeline_config (nipoppy.layout.DatasetLayout attribute) fname_readme (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) force (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow attribute) (nipoppy.workflows.PipelineInstallWorkflow attribute) FORMAT_FILE (in module nipoppy.logger) FORMAT_RICH (in module nipoppy.logger) fpath_config (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_container (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) fpath_curation_status (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_DEFAULT_LAYOUT (in module nipoppy.utils) fpath_demographics (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_HPC_TEMPLATE (in module nipoppy.utils) fpath_layout (nipoppy.workflows.base.BaseDatasetWorkflow attribute) (nipoppy.workflows.BaseDatasetWorkflow attribute) fpath_manifest (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_processing_status (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_SAMPLE_CONFIG (in module nipoppy.utils) FPATH_SAMPLE_DICOM_DIR_MAP (in module nipoppy.utils) FPATH_SAMPLE_MANIFEST (in module nipoppy.utils) fpath_spec (nipoppy.layout.DatasetLayout attribute) G generate_curation_status_table() (in module nipoppy.tabular) (in module nipoppy.tabular.curation_status) generate_fpath_log() (nipoppy.workflows.base.BaseDatasetWorkflow method) (nipoppy.workflows.BaseDatasetWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) GENERATE_PYBIDS_DATABASE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) get_bidsified_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) (nipoppy.tabular.CurationStatusTable method) get_boutiques_config_from_descriptor() (in module nipoppy.config.boutiques) get_completed_participants_sessions() (nipoppy.tabular.processing_status.ProcessingStatusTable method) (nipoppy.tabular.ProcessingStatusTable 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) (nipoppy.tabular.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_fpath_container() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) get_fpaths_to_reorg() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) get_full_path() (nipoppy.layout.DatasetLayout method) get_imaging_subset() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_logger() (in module nipoppy.logger) get_organized_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) (nipoppy.tabular.CurationStatusTable method) get_participants_sessions() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_participants_sessions_to_run() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.ExtractionRunner method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) get_path_info() (nipoppy.layout.LayoutConfig method) get_paths() (nipoppy.layout.DatasetLayout method) get_pipeline_tag() (in module nipoppy.utils) get_pipeline_version() (in module nipoppy.workflows.pipeline) get_record_metadata() (nipoppy.zenodo_api.ZenodoAPI method) get_series_class() (nipoppy.tabular.base.BaseTabular method) get_status() (nipoppy.tabular.curation_status.CurationStatusTable method) (nipoppy.tabular.CurationStatusTable method) get_step_config() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) get_today() (in module nipoppy.utils) get_variables() (nipoppy.config.main.PipelineVariables method) Global config file group (nipoppy.config.pipeline_step.AnalysisLevelType attribute) H handle_bids_source() (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.InitWorkflow method) headers (nipoppy.zenodo_api.ZenodoAPI attribute) HPC hpc (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) hpc_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) HPC_CONFIG_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) HPC_PREAMBLE (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) 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.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) INHERIT (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) invocation (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) INVOCATION_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) is_derived_dicom() (in module nipoppy.workflows.dicom_reorg) is_nipoppy_project() (in module nipoppy.utils) IS_TESTING (in module nipoppy.env) J JSON K keep_workdir (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) L launch_boutiques_run() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) layout (nipoppy.workflows.base.BaseDatasetWorkflow attribute) (nipoppy.workflows.BaseDatasetWorkflow attribute) load() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) (nipoppy.tabular.base.BaseTabular class method) (nipoppy.tabular.Manifest class method) (nipoppy.tabular.manifest.Manifest class method) load_json() (in module nipoppy.utils) load_or_generate() (nipoppy.tabular.dicom_dir_map.DicomDirMap class method) log_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) log_prefix_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stderr (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stdout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) logger (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) M manifest (nipoppy.workflows.base.BaseDatasetWorkflow property) (nipoppy.workflows.BaseDatasetWorkflow property) Manifest file merge() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) mkdir() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) mode (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) model (nipoppy.tabular.base.BaseTabular property) (nipoppy.tabular.curation_status.CurationStatusTable attribute) (nipoppy.tabular.CurationStatusTable attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) model_config (nipoppy.config.BidsPipelineConfig attribute) (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) (nipoppy.config.Config attribute) (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.container.ContainerInfo attribute) (nipoppy.config.ContainerConfig attribute) (nipoppy.config.hpc.HpcConfig attribute) (nipoppy.config.main.Config attribute) (nipoppy.config.main.PipelineVariables attribute) (nipoppy.config.pipeline.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ExtractionPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) (nipoppy.layout.LayoutConfig attribute) (nipoppy.tabular.manifest.ManifestModel attribute) module nipoppy nipoppy.base 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.env nipoppy.layout nipoppy.logger nipoppy.pipeline_validation nipoppy.tabular nipoppy.tabular.base nipoppy.tabular.curation_status nipoppy.tabular.dicom_dir_map nipoppy.tabular.manifest nipoppy.tabular.processing_status nipoppy.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.validate nipoppy.workflows.pipeline_store.zenodo nipoppy.workflows.runner nipoppy.workflows.track_curation nipoppy.workflows.tracker nipoppy.zenodo_api movetree() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) MRI N n_success (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) n_total (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) NAME (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) name (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.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 --verbose --write-list -n -v DATASET_ARGUMENT nipoppy-extract command line option --dataset --dry-run --hpc --keep-workdir --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --simulate --verbose --write-list -n -v DATASET_ARGUMENT nipoppy-init command line option --bids-source --dataset --dry-run --force --layout --mode --verbose -f -n -v DATASET_ARGUMENT nipoppy-pipeline-install command line option --assume-yes --dataset --dry-run --force --layout --overwrite --sandbox --verbose --yes -f -n -v -y DATASET_ARGUMENT SOURCE nipoppy-pipeline-list command line option --dataset DATASET_ARGUMENT nipoppy-pipeline-search command line option --dry-run --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 -n -v -y PIPELINE_DIR nipoppy-pipeline-validate command line option --dry-run --verbose -n -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 --verbose --write-list -n -v DATASET_ARGUMENT nipoppy-reorg command line option --check-dicoms --copy-files --dataset --dry-run --layout --verbose -n -v DATASET_ARGUMENT nipoppy-status command line option --dataset --dry-run --layout --verbose -n -v DATASET_ARGUMENT nipoppy-track-curation command line option --dataset --dry-run --empty --force --layout --regenerate --verbose -f -n -v DATASET_ARGUMENT nipoppy-track-processing command line option --dataset --dry-run --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --verbose -n -v DATASET_ARGUMENT nipoppy.base module nipoppy.base.Base (built-in class) nipoppy.config module nipoppy.config.BasePipelineConfig (built-in class) nipoppy.config.BasePipelineStepConfig (built-in class) nipoppy.config.BidsPipelineConfig (built-in class) nipoppy.config.BidsPipelineStepConfig (built-in class) nipoppy.config.boutiques module nipoppy.config.boutiques.BoutiquesConfig (built-in class) nipoppy.config.BoutiquesConfig (built-in class) nipoppy.config.Config (built-in class) nipoppy.config.container module nipoppy.config.container.ContainerConfig (built-in class) nipoppy.config.container.ContainerInfo (built-in class) nipoppy.config.ContainerConfig (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.BidsPipelineConfig (built-in class) nipoppy.config.pipeline.ExtractionPipelineConfig (built-in class) nipoppy.config.pipeline.PipelineInfo (built-in class) nipoppy.config.pipeline.ProcPipelineConfig (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.ProcPipelineConfig (built-in class) nipoppy.config.ProcPipelineStepConfig (built-in class) nipoppy.config.tracker module nipoppy.config.tracker.TrackerConfig (built-in class) nipoppy.config.TrackerConfig (built-in class) nipoppy.console module nipoppy.env module nipoppy.env.ContainerCommandEnum (built-in class) nipoppy.env.LogColor (built-in class) nipoppy.env.PipelineTypeEnum (built-in class) nipoppy.env.ReturnCode (built-in class) 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.pipeline_validation module 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.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 (built-in class) 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.tabular.ProcessingStatusTable (built-in class) nipoppy.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.BaseDatasetWorkflow (built-in class) nipoppy.workflows.BasePipelineWorkflow (built-in class) nipoppy.workflows.BaseWorkflow (built-in class) nipoppy.workflows.bids_conversion module nipoppy.workflows.bids_conversion.BidsConversionRunner (built-in class) nipoppy.workflows.BidsConversionRunner (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.DicomReorgWorkflow (built-in class) nipoppy.workflows.ExtractionRunner (built-in class) nipoppy.workflows.extractor module nipoppy.workflows.extractor.ExtractionRunner (built-in class) nipoppy.workflows.InitWorkflow (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.validate module nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow (built-in class) nipoppy.workflows.pipeline_store.zenodo module nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow (built-in class) nipoppy.workflows.PipelineInstallWorkflow (built-in class) nipoppy.workflows.PipelineListWorkflow (built-in class) nipoppy.workflows.PipelineRunner (built-in class) nipoppy.workflows.PipelineTracker (built-in class) nipoppy.workflows.PipelineValidateWorkflow (built-in class) nipoppy.workflows.runner module nipoppy.workflows.runner.PipelineRunner (built-in class) nipoppy.workflows.StatusWorkflow (built-in class) nipoppy.workflows.track_curation module nipoppy.workflows.track_curation.TrackCurationWorkflow (built-in class) nipoppy.workflows.TrackCurationWorkflow (built-in class) nipoppy.workflows.tracker module nipoppy.workflows.tracker.PipelineTracker (built-in class) nipoppy.zenodo_api module nipoppy.zenodo_api.InvalidChecksumError nipoppy.zenodo_api.ZenodoAPI (built-in class) nipoppy.zenodo_api.ZenodoAPIError NIPOPPY_DIR_NAME (in module nipoppy.env) NO_PARTICIPANTS_OR_SESSIONS_TO_RUN (nipoppy.env.ReturnCode attribute) P PARTIAL_SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode 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.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) participant_id_to_bids_participant_id() (in module nipoppy.utils) participant_session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) PARTICIPANT_SESSION_DIR (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) password_file (nipoppy.zenodo_api.ZenodoAPI attribute) 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) (nipoppy.config.TrackerConfig attribute) pipeline_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PIPELINE_DIR nipoppy-pipeline-upload command line option pipeline_dir (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) pipeline_name (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_step (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_step_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PIPELINE_TYPE (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) PIPELINE_TYPE_TO_CLASS (in module nipoppy.pipeline_validation) pipeline_type_to_dname_map (nipoppy.layout.DatasetLayout attribute) PIPELINE_VARIABLES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) pipeline_version (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) prepare_container() (in module nipoppy.config.container) PROC_DEPENDENCIES (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) proc_pipeline_info (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) PROC_PIPELINES process_container_config() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) process_template_json() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) process_template_str() (in module nipoppy.utils) PROCESSING (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) Processing status file processing_status_table (nipoppy.workflows.base.BaseDatasetWorkflow property) (nipoppy.workflows.BaseDatasetWorkflow property) PROGRAM_NAME (in module nipoppy.env) propagate_container_config_to_pipeline() (nipoppy.config.Config method) (nipoppy.config.main.Config method) PYBIDS_IGNORE_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) pybids_ignore_patterns (nipoppy.workflows.BasePipelineWorkflow property) (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.zenodo.ZenodoUploadWorkflow attribute) regenerate (nipoppy.workflows.track_curation.TrackCurationWorkflow attribute) (nipoppy.workflows.TrackCurationWorkflow attribute) return_code (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) rm() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_cleanup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.InitWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.track_curation.TrackCurationWorkflow method) (nipoppy.workflows.TrackCurationWorkflow method) (nipoppy.workflows.tracker.PipelineTracker method) run_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_main() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dataset_status.StatusWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.InitWorkflow 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.validate.PipelineValidateWorkflow method) (nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow method) (nipoppy.workflows.PipelineInstallWorkflow method) (nipoppy.workflows.PipelineListWorkflow method) (nipoppy.workflows.PipelineValidateWorkflow method) (nipoppy.workflows.StatusWorkflow method) (nipoppy.workflows.track_curation.TrackCurationWorkflow method) (nipoppy.workflows.TrackCurationWorkflow method) run_setup() (nipoppy.workflows.base.BaseDatasetWorkflow method) (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseDatasetWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_single() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.ExtractionRunner method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) S sandbox (nipoppy.zenodo_api.ZenodoAPI attribute) save() (nipoppy.config.Config method) (nipoppy.config.main.Config method) save_df_with_backup() (in module nipoppy.utils) save_json() (in module nipoppy.utils) save_tabular_file() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) save_with_backup() (nipoppy.tabular.base.BaseTabular method) SCHEMA_VERSION (nipoppy.config.BasePipelineConfig attribute) (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.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) session_id_to_bids_session_id() (in module nipoppy.utils) session_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) SESSIONS set_authorization() (nipoppy.zenodo_api.ZenodoAPI method) set_container_env_vars() (in module nipoppy.config.container) set_logger() (nipoppy.zenodo_api.ZenodoAPI method) set_status() (nipoppy.tabular.curation_status.CurationStatusTable method) (nipoppy.tabular.CurationStatusTable method) set_up_bids_db() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) set_variables() (nipoppy.config.main.PipelineVariables method) simulate (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner 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) (nipoppy.workflows.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) (nipoppy.tabular.CurationStatusTable attribute) STATUS_FAIL (in module nipoppy.tabular.processing_status) status_fail (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) STATUS_INCOMPLETE (in module nipoppy.tabular.processing_status) status_incomplete (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) STATUS_SUCCESS (in module nipoppy.tabular.processing_status) status_success (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) STATUS_UNAVAILABLE (in module nipoppy.tabular.processing_status) status_unavailable (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) (nipoppy.tabular.ProcessingStatusTable attribute) STEP (nipoppy.config.pipeline.PipelineInfo attribute) STEPS (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.BidsPipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) StrOrPathLike (in module nipoppy.env) SUBSTITUTIONS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) T tar (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) tar_directory() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) TEMPLATE_PIPELINE_PATH (in module nipoppy.utils) TEMPLATE_REPLACE_PATTERN (in module nipoppy.utils) Tracker config file tracker_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) TRACKER_CONFIG_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) type_ (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) U UNKNOWN_FAILURE (nipoppy.env.ReturnCode attribute) update_curation_status_table() (in module nipoppy.tabular) (in module nipoppy.tabular.curation_status) UPDATE_STATUS (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) upload_pipeline() (nipoppy.zenodo_api.ZenodoAPI method) URI (nipoppy.config.container.ContainerInfo attribute) V validate() (nipoppy.layout.DatasetLayout method) (nipoppy.tabular.base.BaseTabular method) (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) validate_after() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.BasePipelineStepConfig method) (nipoppy.config.BidsPipelineStepConfig method) (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.pipeline_step.ProcPipelineStepConfig method) (nipoppy.config.ProcPipelineStepConfig method) (nipoppy.config.tracker.TrackerConfig method) (nipoppy.config.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.Config method) (nipoppy.config.main.Config method) validate_before() (nipoppy.config.BasePipelineConfig class method) (nipoppy.config.BasePipelineStepConfig class method) (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.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) venv verbose (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) VERSION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) Visit ID visit_id (nipoppy.tabular.manifest.ManifestModel attribute) visit_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) VISITS W write_list (nipoppy.workflows.BasePipelineWorkflow attribute) (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.zenodo.ZenodoUploadWorkflow attribute) (nipoppy.workflows.PipelineInstallWorkflow attribute) zenodo_id (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) (nipoppy.workflows.PipelineInstallWorkflow attribute)