Profiles¶
To select one or multiple profiles, please use the -profile
option. For example:
$> nextflow run tractoflow -r 2.4.0 --input input_folder -profile macos,fully_reproducible -with-singularity singularity_name.sif -resume
Profiles available¶
macos
- When this profile is used, TractoFlow will modify a parameter (scratch) for MacOS users.
use_cuda
- When this profile is used, TractoFlow will use eddy_cuda for Eddy process. This feature is available with NVidia GPUs only. Without this profile, TractoFlow will run eddy_openmp.
fully_reproducible
- When this profile is used, all the parameters will be set to have 100% reproducible results. This profile consist to set multi-thread parameters to be fully reproducible [Theaud20].
cbrain
- When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.
ABS
- When this profile is used, TractoFlow-ABS (Atlas Based Segmentation) is used. This profile must be used for pathological data. The aparc+aseg.nii.gz and wmparc.nii.gz must be in the same space than t1.nii.gz
bundling
- When this profile is used, it will activate custom tracking parameters to improve recobundle results.
connectomics
- When this profile is used, it will activate custom tracking parameters to improve connectomics analysis.