USAGE

SCIL dMRI pipeline
==================

Run human pipeline

USAGE

nextflow run main.nf [OPTIONAL ARGUMENTS] (--input) (-profile)

DESCRIPTION

    --input=/path/to/[root]             Input folder containing tractoflow input (bids structure or not)
                                        or TractoFlow or RBX results folder.

PROFILES (using -profile option (e.g. -profile tractoflow_qc_light,cbrain))

    input_qc                            Create QC reports for your raw data (Can be a BIDS structure).

    tractoflow_qc_light                 Create QC reports for your TractoFlow results:
                                        Output important steps only.

    tractoflow_qc_all                   Create QC reports for your TractoFlow results:
                                        Output all steps.

    rbx_qc                              Create QC reports for your rbx-flow results.

    disconets_qc                       Create QC reports for your disconets_flow results.

    cbrain                              When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.
                                        cbrain profile should be used as a second profile (e.g -profile input_qc,cbrain).

OPTIONAL ARGUMENTS (current value)

    --dicom_fields                      All dicom fields extracted to QC the DWI protocol - Works only with profile input_qc (--dicom_fields "$dicom_fields").

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

Files should be compressed Nifti files (.nii.gz)

NOTES

The intermediate working directory is, by default, set to './work'.
To change it, use the '-w WORK_DIR' argument.

The default config file is pipeline_human/nextflow.config.
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 ...'.