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conp-pipeline

conp-pipeline is a tool that runs pipelines and commits their inputs and results to a DataLad dataset.

Installation

  • Install git-annex
  • pip install git+https://github.com/datalad/datalad.git
  • pip install conp-pipeline

Syntax

conp-pipeline run <dataset> <descriptor> <invocation>

Example

The following commands create a test DataLad dataset, run FSL bet on a test image and commit the results to the dataset.

datalad create test-dataset
conp-pipeline run test-dataset tests/fsl_bet.json tests/invocation.json

Metadata

conp-pipeline run adds the following metadata to the pipeline inputs and outputs:

  • <descriptor>:
    • conp-pipeline-role: pipeline-description
    • various fields extracted from the Boutiques descriptor including name, description, tags, container-type, etc.
  • <invocation>: conp-pipeline-role: invocation-description.
  • Pipeline input files: conp-pipeline-role: input-file.
  • Pipeline results: conp-pipeline-role: result-file.