shell:
    'node {params.script} --base-url {params.in_url} --subject {wildcards.subject} --stain {wildcards.stain} --dspow  {params.dspow} --out-dir {output.raw_dir}'

shell:
    'ls {input}/*.jpg | wc -l > {output}'

shell:
    '{input.conform_script} {input.slice_dir} {output.slice_dir}'

shell:
    'c3d {input.slice_dir}/* -tile z -spacing {params.spacing} -orient {params.orient} {output.stack}' 

shell:
    'c3d {input.stack} -threshold 230 Inf 0 1 {output.mask}' 

shell:
    'c3d {input.template} -cmv -pop -pop  -thresh 50% inf 0 1 -as MASK {input.template} -times -o {output.hemi}'

shell:
    'c3d_affine_tool {input} -inv -o {output}'

shell:
    'greedy -threads {threads} -d 3 -r {input.xfm} -rf {input.fixed} -rm {input.moving} {output.warped} > {log}'

shell:
    'c3d {input} -slice z {wildcards.slice} -o {output}'

shell:
    'c3d {input} -slice z {wildcards.slice} -o {output}'

shell:
    'greedy -threads {threads} -d 2 -i {input.template_slice} {input.hist_slice} -o {output.moment_xfm} {params.moment_opts} > {log} && ' 
    'greedy -threads {threads} -d 2 -i {input.template_slice} {input.hist_slice} -o {output.affine_xfm} -ia {output.moment_xfm} {params.affine_opts} >> {log} && ' 
    'greedy -threads {threads} -d 2 -i {input.template_slice} {input.hist_slice} -o {output.nlin_warp} -it {output.affine_xfm} {params.nlin_opts} >> {log} && '
    'greedy -threads {threads} -d 2 -r {output.nlin_warp} {output.affine_xfm} -rf {input.template_slice} -rm {input.hist_slice} {output.hist_warped} >> {log} '

shell:
    'c3d {input.hist_slices} -tile z -spacing {params.spacing} -orient {params.orient} {output.hist_stack}'