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.BidsConversionRunner 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.BidsConversionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.runner.PipelineRunner 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) 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.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow 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.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) handle_exception() (in module nipoppy.cli) 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.PipelineRunner attribute) L launch_boutiques_run() (nipoppy.workflows.runner.PipelineRunner 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.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.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.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.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.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.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.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.runner module nipoppy.workflows.runner.PipelineRunner (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.InvalidChecksumError 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.BidsConversionRunner 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.BidsConversionRunner 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.PipelineRunner 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) 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.BidsConversionRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.runner.PipelineRunner 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.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_single() (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.runner.PipelineRunner 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.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) 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.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.ProcPipelineConfig 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.runner.PipelineRunner attribute) tar_directory() (nipoppy.workflows.runner.PipelineRunner method) TEMPLATE_PIPELINE_PATH (in module nipoppy.utils.utils) TEMPLATE_REPLACE_PATTERN (in module nipoppy.utils.utils) 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)