USAGE

Pipeline for FINTA MultiBundle
======================================

USAGE

nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]


DESCRIPTION

    --input=/path/to/[root]              Root folder containing multiple subjects

                                        [root]
                                        ├── S1
                                        |   ├── S1_0
                                        |   |   └── Register_Streamlines
                                        |   |       └── *.trk
                                        |   ├── S1_1
                                        |   ├── S1_2
                                        |   └── S1_3
                                        └── S2
                                            └── *

    --subjects_config                    Path to subject config
    --bundles_config                     Path to bundle config

    OPTIONAL ARGUMENTS (current value)

    --processes                             The number of parallel processes to launch ($cpu_count).
                                            Only affects the local scheduler.

    --output_dir                            Directory where to write the final results.
                                            By default, will be in "./results"

NOTES

Use '-C config_file.config' to specify a non-default configuration file.
The '-C config_file.config' must be inserted after the nextflow call
like 'nextflow -C config_file.config run ...'.