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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
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    - nipoppy.config.hpc
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      - nipoppy.config.hpc.HpcConfig
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      - nipoppy.config.main.Config
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    - 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
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    - nipoppy.config.BidsPipelineStepConfig
    - nipoppy.config.BoutiquesConfig
    - nipoppy.config.Config
    - nipoppy.config.ContainerConfig
    - nipoppy.config.ProcPipelineConfig
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  - nipoppy.console
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  - nipoppy.layout
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  - nipoppy.logger
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    - nipoppy.tabular.manifest
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  - nipoppy.utils
  - nipoppy.workflows
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    - nipoppy.workflows.base
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      - nipoppy.workflows.bids_conversion.BidsConversionRunner
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      - nipoppy.workflows.dataset_init.InitWorkflow
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        nipoppy.workflows.pipeline_store.list.PipelineListWorkflow
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        nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow
    - nipoppy.workflows.runner
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    - nipoppy.workflows.track_curation
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    - nipoppy.workflows.BaseDatasetWorkflow
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File schemas

Other

What’s new
Contributing
Glossary

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nipoppy.workflows.bids_conversion¶

Workflow for convert command.

Classes¶

BidsConversionRunner

Convert data to BIDS.

nipoppy.workflows.bids_conversion.BidsConversionRunner

nipoppy.workflows.base.BaseWorkflow

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