Sample Snakefile for MDT

config.yml

in_dir: '/project/6007967/akhanf/projects/hcp/HCP_1200_T1w_Diffusion_FS'

container: '/project/6050199/akhanf/singularity/bids-apps/khanlab_mdt-bids_v0.1.sif'

#paths to inputs, relative to in_dir
bvec: '{subject}/T1w/Diffusion/bvecs'
bval: '{subject}/T1w/Diffusion/bvals'
dwi: '{subject}/T1w/Diffusion/data.nii.gz'
grad_dev: '{subject}/T1w/Diffusion/grad_dev.nii.gz'

Snakefile

from os.path import join

configfile: 'config.yml'

container: config['container']


rule create_protocol:
    input:
        bvec = join(config['in_dir'],config['bvec']),
        bval = join(config['in_dir'],config['bval'])
    output:
        protocol = 'results/{subject}/{subject}.prtcl'
    shell: 'mdt-create-protocol -o {output} {input.bvec} {input.bval}'

run with: https://github.com/khanlab/cc-slurm