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Overview

Why Nipoppy?
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- The principles
- The use cases
Installation
Quickstart

How-to guides

User guide (legacy)
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Initializing a new dataset
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- Starting with non-BIDS data
- Starting with BIDS data
Adding a pipeline to a dataset
Running a pipeline

Reference

Command-line interface
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Python API
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- nipoppy
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  - nipoppy.base
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    - nipoppy.base.Base
  - nipoppy.config
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    - nipoppy.config.boutiques
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      - nipoppy.config.boutiques.BoutiquesConfig
    - nipoppy.config.container
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      - nipoppy.config.container.ContainerConfig
      - nipoppy.config.container.ContainerInfo
    - nipoppy.config.hpc
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      - nipoppy.config.hpc.HpcConfig
    - nipoppy.config.main
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      - nipoppy.config.main.Config
      - nipoppy.config.main.PipelineVariables
    - nipoppy.config.pipeline
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    - nipoppy.config.pipeline_step
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    - nipoppy.config.tracker
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      - nipoppy.config.tracker.TrackerConfig
    - nipoppy.config.BasePipelineConfig
    - nipoppy.config.BasePipelineStepConfig
    - nipoppy.config.BidsPipelineConfig
    - nipoppy.config.BidsPipelineStepConfig
    - nipoppy.config.BoutiquesConfig
    - nipoppy.config.Config
    - nipoppy.config.ContainerConfig
    - nipoppy.config.ProcPipelineConfig
    - nipoppy.config.ProcPipelineStepConfig
    - nipoppy.config.TrackerConfig
  - nipoppy.console
  - nipoppy.env
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  - nipoppy.layout
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  - nipoppy.logger
  - nipoppy.pipeline_validation
  - nipoppy.tabular
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    - nipoppy.tabular.base
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      - nipoppy.tabular.base.BaseTabular
      - nipoppy.tabular.base.BaseTabularModel
    - nipoppy.tabular.curation_status
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      - nipoppy.tabular.curation_status.CurationStatusModel
      - nipoppy.tabular.curation_status.CurationStatusTable
    - nipoppy.tabular.dicom_dir_map
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      - nipoppy.tabular.dicom_dir_map.DicomDirMap
      - nipoppy.tabular.dicom_dir_map.DicomDirMapModel
    - nipoppy.tabular.manifest
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      - nipoppy.tabular.manifest.Manifest
      - nipoppy.tabular.manifest.ManifestModel
    - nipoppy.tabular.processing_status
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      - nipoppy.tabular.processing_status.ProcessingStatusModel
      - nipoppy.tabular.processing_status.ProcessingStatusTable
    - nipoppy.tabular.CurationStatusTable
    - nipoppy.tabular.Manifest
    - nipoppy.tabular.ProcessingStatusTable
  - nipoppy.utils
  - nipoppy.workflows
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    - nipoppy.workflows.base
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      - nipoppy.workflows.base.BaseDatasetWorkflow
      - nipoppy.workflows.base.BaseWorkflow
    - nipoppy.workflows.bids_conversion
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      - nipoppy.workflows.bids_conversion.BidsConversionRunner
    - nipoppy.workflows.dataset_init
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      - nipoppy.workflows.dataset_init.InitWorkflow
    - nipoppy.workflows.dataset_status
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      - nipoppy.workflows.dataset_status.StatusWorkflow
    - nipoppy.workflows.dicom_reorg
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      - nipoppy.workflows.dicom_reorg.DicomReorgWorkflow
    - nipoppy.workflows.extractor
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      - nipoppy.workflows.extractor.ExtractionRunner
    - nipoppy.workflows.pipeline
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      - nipoppy.workflows.pipeline.BasePipelineWorkflow
    - nipoppy.workflows.pipeline_store
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      - nipoppy.workflows.pipeline_store.create
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        nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow
      - nipoppy.workflows.pipeline_store.install
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        nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow
      - nipoppy.workflows.pipeline_store.list
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        nipoppy.workflows.pipeline_store.list.PipelineListWorkflow
      - nipoppy.workflows.pipeline_store.search
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        nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow
      - nipoppy.workflows.pipeline_store.validate
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        nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow
      - nipoppy.workflows.pipeline_store.zenodo
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        nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow
    - nipoppy.workflows.runner
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      - nipoppy.workflows.runner.PipelineRunner
    - nipoppy.workflows.track_curation
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      - nipoppy.workflows.track_curation.TrackCurationWorkflow
    - nipoppy.workflows.tracker
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      - nipoppy.workflows.tracker.PipelineTracker
    - nipoppy.workflows.BaseDatasetWorkflow
    - nipoppy.workflows.BasePipelineWorkflow
    - nipoppy.workflows.BaseWorkflow
    - nipoppy.workflows.BidsConversionRunner
    - nipoppy.workflows.DicomReorgWorkflow
    - nipoppy.workflows.ExtractionRunner
    - nipoppy.workflows.InitWorkflow
    - nipoppy.workflows.PipelineInstallWorkflow
    - nipoppy.workflows.PipelineListWorkflow
    - nipoppy.workflows.PipelineRunner
    - nipoppy.workflows.PipelineTracker
    - nipoppy.workflows.PipelineValidateWorkflow
    - nipoppy.workflows.StatusWorkflow
    - nipoppy.workflows.TrackCurationWorkflow
  - nipoppy.zenodo_api
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File schemas

Other

What’s new
Contributing
Glossary

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nipoppy.workflows.runner¶

PipelineRunner workflow.

Classes¶

PipelineRunner

Pipeline runner.

nipoppy.workflows.runner.PipelineRunner

nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow

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