Index

Symbols

--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-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option --dry-run nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option --empty nipoppy-track-curation command line option --force nipoppy-track-curation command line option --keep-workdir nipoppy-run command line option --layout nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option --mode nipoppy-init command line option --participant-id nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option nipoppy-track command line option --pipeline nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option nipoppy-track command line option --pipeline-step nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option nipoppy-track command line option

--pipeline-version nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option nipoppy-track command line option --regenerate nipoppy-track-curation command line option --session-id nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option nipoppy-track command line option --simulate nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option --tar nipoppy-run command line option --verbose nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option --version nipoppy command line option --write-list nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-run command line option -f nipoppy-track-curation command line option -n nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option -v nipoppy-bidsify command line option nipoppy-extract command line option nipoppy-init command line option nipoppy-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option

A

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

apply_analysis_level() (in module nipoppy.workflows.pipeline) apply_fname_mapping() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) apply_substitutions_to_json() (in module nipoppy.utils) (nipoppy.config.Config method) (nipoppy.config.main.Config method) 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)

B

BIDS bids_participant_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) BIDS_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) bids_session_id (nipoppy.tabular.processing_status.ProcessingStatusModel attribute) BIDS_SESSION_PREFIX (in module nipoppy.env)

bids_source (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) BIDS_SUBJECT_PREFIX (in module nipoppy.env) 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_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.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) 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_symlink() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) Curation status file curation_status_table (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) 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-reorg command line option nipoppy-run command line option nipoppy-status command line option nipoppy-track command line option nipoppy-track-curation command line option DATASET_NAME (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) 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.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow 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_pipeline_idp (nipoppy.layout.DatasetLayout attribute) dname_pipeline_output (nipoppy.layout.DatasetLayout attribute) 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_LAYOUTS (in module nipoppy.utils) dpath_logs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig 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) dpath_pipeline_bids_db (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.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) DPATH_SAMPLE_PIPELINES (in module nipoppy.utils) 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 (nipoppy.layout.DatasetLayout property) 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_TAR (in module nipoppy.env) EXTRACTION_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config 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_readme (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow 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_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow 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_CONFIG_FULL (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) fpaths (nipoppy.layout.DatasetLayout property)

G

generate_curation_status_table() (in module nipoppy.tabular) (in module nipoppy.tabular.curation_status) generate_fpath_log() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow 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_idp() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_output() (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_config() (in module nipoppy.config.main) get_pipeline_tag() (in module nipoppy.utils) get_pipeline_version() (in module nipoppy.config.main) 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) group (nipoppy.config.pipeline_step.AnalysisLevelType attribute)

H

HPC

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_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.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow 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) LOG_SUFFIX (in module nipoppy.workflows.base) logger (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute)

M

manifest (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) 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.main.Config 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.main nipoppy.config.pipeline nipoppy.config.pipeline_step nipoppy.config.tracker nipoppy.env nipoppy.layout nipoppy.logger 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.runner nipoppy.workflows.track_curation nipoppy.workflows.tracker 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 --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 --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 --layout --mode --verbose -n -v DATASET_ARGUMENT nipoppy-reorg command line option --check-dicoms --copy-files --dataset --dry-run --layout --verbose -n -v DATASET_ARGUMENT nipoppy-run command line option --dataset --dry-run --keep-workdir --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --simulate --tar --verbose --write-list -n -v DATASET_ARGUMENT nipoppy-status command line option --dataset --dry-run --layout --verbose -n -v DATASET_ARGUMENT nipoppy-track command line option --dataset --dry-run --layout --participant-id --pipeline --pipeline-step --pipeline-version --session-id --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.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.main module nipoppy.config.main.Config (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.env module nipoppy.env.LogColor (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.OptionalFpathInfo (built-in class) nipoppy.layout.PathInfo (built-in class) nipoppy.logger 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.BaseWorkflow (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.PipelineRunner (built-in class) nipoppy.workflows.PipelineTracker (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)

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) path (nipoppy.layout.PathInfo attribute) path_infos (nipoppy.layout.LayoutConfig property) path_labels (nipoppy.layout.LayoutConfig property) path_sep (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) 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_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_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 (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) 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 status file processing_status_table (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) PROGRAM_NAME (in module nipoppy.env) propagate_container_config() (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

R

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.StatusWorkflow method) (nipoppy.workflows.track_curation.TrackCurationWorkflow method) (nipoppy.workflows.TrackCurationWorkflow method)

run_setup() (nipoppy.workflows.base.BaseWorkflow 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

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) 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.config.Config attribute) (nipoppy.config.main.Config attribute) session_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) SESSIONS set_container_env_vars() (in module nipoppy.config.container) 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) simulate (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) sort_values() (nipoppy.tabular.base.BaseTabular method)

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_REPLACE_PATTERN (in module nipoppy.utils)

tracker_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) TRACKER_CONFIG_FILE (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute)

U

UNKOWN_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) 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.pipeline.BasePipelineConfig method) (nipoppy.config.pipeline.ExtractionPipelineConfig 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)

validate_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow 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.config.Config attribute) (nipoppy.config.main.Config 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)