TIGRLab Pipelines: Utterly Reproducible Research (TIGR-PURR)

Welcome to the documentation page for TIGR-PURR. This is where you’ll find information about how to run the lab’s supported pipelines yourself as well as the various configuration options available to you.

TIGR-PURR is a pipeline system based off a combination of Nextflow and Boutiques which allow us to seamlessly run a variety of BIDS Applications based distributed pipelines easily with only a little bit of configuration work. The system will allow you to run full BIDS-app pipelines on:

• The local Kimel-Lab Cluster
• CAMH’s SCC Cluster
• Scinet’s Niagara Cluster
• Your local computer

To learn about how you can run BIDS pipelines on any BIDS dataset go to Getting started

To go through a quick example that you can run yourself, check out the quickstart tutorials.

Contents

• Getting started
  • Default Pipelines
  • Running your own Default Pipeline
  • Cleaning the Nextflow Work folder
  • Running BIDS-apps with Custom Arguments
  • Pipeline Dry-Runs
  • Running Only Specific Subjects
  • Making Pipeline Run Reports
  • Pipeline Logging
  • Running Pipelines on Other Systems (SCC/Scinet/Local)
  • Customizing SLURM Directives (Advanced)
• TIGR-PURR Quickstart Tutorial
  • Setting up the Quickstart Tutorial
  • Dry-Runs of Pipelines
  • Running the pipeline
  • Cleaning up your TIGR-PURR run
• Quick Reference Guide to Pipeline Usage
  • Default Pipeline Outputs
  • Running a Default Pipeline
  • Running a subset of subjects
  • Using custom BIDS-app arguments
  • Running on other clusters
  • Using custom SLURM directives
• Non-BIDS (TIGRLAB-specific) Pipelines
  • FeenICS
  • FieldMaps
• Upcoming Features
  • v1.1 Release Notes
• Changes
  • v1.0.1