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-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-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 --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-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 -v 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-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) 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.utils) add_path_timestamp() (in module nipoppy.utils.utils) add_pybids_ignore_patterns() (in module nipoppy.utils.bids) alias_map (nipoppy.cli.OrderedAliasedGroup attribute) ANALYSIS_LEVEL (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) apply_pipeline_variables() (nipoppy.config.main.Config method) apply_substitutions_to_json() (in module nipoppy.utils.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) 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_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) BIDS_SUBJECT_PREFIX (in module nipoppy.env) BIDSIFICATION (nipoppy.config.main.PipelineVariables attribute) (nipoppy.env.PipelineTypeEnum attribute) Boutiques boutiques_config (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) check_dir() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) 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 col_bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusTable attribute) col_datatype (nipoppy.tabular.manifest.Manifest 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_visit_id (nipoppy.tabular.manifest.Manifest attribute) COMMAND (nipoppy.config.container.ContainerConfig attribute) concatenate() (nipoppy.tabular.base.BaseTabular method) conda config (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseDatasetWorkflow property) CONSOLE_STDERR (in module nipoppy.console) CONSOLE_STDOUT (in module nipoppy.console) CONTAINER_CONFIG CONTAINER_INFO (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) copy() (nipoppy.workflows.base.BaseWorkflow method) copy_files (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) copytree() (nipoppy.workflows.base.BaseWorkflow method) create_bids_db() (in module nipoppy.utils.bids) create_bundle() (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow method) create_symlink() (nipoppy.workflows.base.BaseWorkflow method) Curation status file curation_status_table (nipoppy.workflows.base.BaseDatasetWorkflow property) CURRENT_SCHEMA_VERSION (in module nipoppy.env) CUSTOM (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 dataset_option() (in module nipoppy.cli.options) 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) 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) dname_hpc_logs (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.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) 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 empty (nipoppy.workflows.track_curation.TrackCurationWorkflow 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.env.LogColor attribute) FAKE_SESSION_ID (in module nipoppy.env) FIELD_DESCRIPTION_MAP (in module nipoppy.utils.utils) FILE (nipoppy.config.container.ContainerInfo attribute) find_duplicates() (nipoppy.tabular.base.BaseTabular 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) 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.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_HPC_TEMPLATE (in module nipoppy.utils.utils) fpath_layout (nipoppy.workflows.base.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.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_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_bidsified_participants_sessions() (nipoppy.tabular.curation_status.CurationStatusTable method) get_boutiques_config_from_descriptor() (in module nipoppy.config.boutiques) get_command() (nipoppy.cli.OrderedAliasedGroup method) get_completed_participants_sessions() (nipoppy.tabular.processing_status.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) 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.pipeline.BasePipelineConfig 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_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_pipeline_tag() (in module nipoppy.utils.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) get_step_config() (nipoppy.config.pipeline.BasePipelineConfig 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) headers (nipoppy.zenodo_api.ZenodoAPI attribute) HPC hpc (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) hpc_config (nipoppy.workflows.pipeline.BasePipelineWorkflow property) HPC_CONFIG_FILE (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) HPC_PREAMBLE (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.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.env.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_nipoppy_project() (in module nipoppy.utils.utils) IS_TESTING (in module nipoppy.env) J JOBLIB_INSTALLED (in module nipoppy.workflows.pipeline) JSON K keep_workdir (nipoppy.workflows.runner.Runner attribute) L launch_boutiques_run() (nipoppy.workflows.runner.Runner method) layout (nipoppy.workflows.base.BaseDatasetWorkflow attribute) layout_option() (in module nipoppy.cli.options) list_commands() (nipoppy.cli.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) log_command() (nipoppy.workflows.base.BaseWorkflow method) log_prefix_run (nipoppy.workflows.base.BaseWorkflow attribute) log_prefix_run_stderr (nipoppy.workflows.base.BaseWorkflow attribute) log_prefix_run_stdout (nipoppy.workflows.base.BaseWorkflow attribute) logger (in module nipoppy.cli) (nipoppy.workflows.base.BaseWorkflow attribute) M manifest (nipoppy.workflows.base.BaseDatasetWorkflow property) Manifest file merge() (nipoppy.config.container.ContainerConfig method) MISSING_DEPENDENCY (nipoppy.cli.ReturnCode attribute) (nipoppy.env.ReturnCode attribute) mkdir() (nipoppy.workflows.base.BaseWorkflow method) 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.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.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.utils.bids 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.track_curation nipoppy.workflows.tracker nipoppy.zenodo_api movetree() (nipoppy.workflows.base.BaseWorkflow method) 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) 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 DATASET_ARGUMENT 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 DATASET_ARGUMENT nipoppy-init command line option --bids-source --dataset --dry-run --force --layout --mode --verbose -f -v DATASET_ARGUMENT nipoppy-pipeline-install command line option --assume-yes --dataset --dry-run --force --layout --overwrite --sandbox --verbose --yes -f -v -y DATASET_ARGUMENT SOURCE nipoppy-pipeline-list command line option --dataset --dry-run --layout --verbose -v 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 -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 DATASET_ARGUMENT nipoppy-reorg command line option --check-dicoms --copy-files --dataset --dry-run --layout --verbose -v DATASET_ARGUMENT nipoppy-status command line option --dataset --dry-run --layout --verbose -v DATASET_ARGUMENT nipoppy-track-curation command line option --dataset --dry-run --empty --force --layout --regenerate --verbose -f -v DATASET_ARGUMENT nipoppy-track-processing command line option --dataset --dry-run --layout --n-jobs --participant-id --pipeline --pipeline-step --pipeline-version --session-id --verbose -v DATASET_ARGUMENT nipoppy.base module nipoppy.base.Base (built-in class) nipoppy.cli module nipoppy.cli.options module nipoppy.cli.OrderedAliasedGroup (built-in class) 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.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.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.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.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.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.env.ReturnCode attribute) P PARTIAL_SUCCESS (nipoppy.cli.ReturnCode attribute) (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.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) 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-upload command line option pipeline_dir (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow 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) 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) 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) prepare_container() (in module nipoppy.config.container) PROC_DEPENDENCIES (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) proc_pipeline_info (nipoppy.workflows.extractor.ExtractionRunner property) PROC_PIPELINES 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.workflows.base.BaseDatasetWorkflow property) PROGRAM_NAME (in module nipoppy.cli) (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) return_code (nipoppy.workflows.base.BaseWorkflow attribute) rm() (nipoppy.workflows.base.BaseWorkflow method) run() (nipoppy.workflows.base.BaseWorkflow method) run_cleanup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.bids_conversion.BIDSificationRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.processing_runner.ProcessingRunner method) (nipoppy.workflows.track_curation.TrackCurationWorkflow method) (nipoppy.workflows.tracker.PipelineTracker method) run_command() (nipoppy.workflows.base.BaseWorkflow method) run_main() (nipoppy.workflows.base.BaseWorkflow 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) 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) 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_tabular_file() (nipoppy.workflows.base.BaseWorkflow method) 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) 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) set_up_bids_db() (nipoppy.workflows.pipeline.BasePipelineWorkflow method) set_variables() (nipoppy.config.main.PipelineVariables 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) StrOrPathLike (in module nipoppy.env) SUBSTITUTIONS (nipoppy.config.main.Config attribute) SUCCESS (nipoppy.cli.ReturnCode attribute) (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) success() (in module nipoppy.logger) 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) 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) type_ (nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow attribute) U UNKNOWN_FAILURE (nipoppy.cli.ReturnCode attribute) (nipoppy.env.ReturnCode attribute) update_curation_status_table() (in module nipoppy.tabular.curation_status) UPDATE_STATUS (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) upload_pipeline() (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.pipeline_step.ProcPipelineStepConfig 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) 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) VISITS W 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_id (nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow attribute) zenodo_options() (in module nipoppy.cli.pipeline_catalog)