notes

configfile: "config/config.yaml" 

print(config['hippunfoldData'])

rule all:
    input: 'sub-P022_space-T1w_den-0p5mm_label-hipp_surfaces.spec'

rule hippunfold_exc:
    input:
        bids_dir = ('/home/ROBARTS/mcespedes/graham/projects/ctb-akhanf/akhanf/cfmm-bids/data/Khan/SNSX_7T/tar2bids_v0.0.5e/correct7T.v0.3')
    params:
        patients = config['hippunfoldData'],
        o_dir = '/home/ROBARTS/mcespedes/scratch/Results/'
    output:
        'sub-P022_space-T1w_den-0p5mm_label-hipp_surfaces.spec'
    shell:
        ('hippunfold {input.bids_dir} {params.o_dir} participant --participant_label {params.patients} -n'
         '--modality T1w --use-singularity --singularity-prefix $SNAKEMAKE_SINGULARITY_DIR')



snsx_patients: >
                sub-P022 sub-P026 sub-P029 sub-P032 sub-P046 sub-P048 sub-P049 sub-P051
                sub-P052 sub-P054 sub-P055 sub-P056 sub-P058 sub-P059 sub-P060 sub-P061
                sub-P070 sub-P071 sub-P080 sub-P081 sub-P087 sub-P089 sub-P090 sub-P092
                sub-P095 sub-P097 sub-P100
clinical_patients: > 
                sub-P002 sub-P003 sub-P016 sub-P004	sub-P001 sub-P007 sub-P009 sub-P013
                sub-P018 sub-P022 sub-P021 sub-P023 sub-P065 sub-P067 sub-P068 sub-P069
                sub-P078 sub-P079 sub-P081 sub-P082 sub-P083 sub-P086 sub-P087 sub-P088
                sub-P091 sub-P093 sub-P095