fix shells and lmax argurments

- adds necessary changes to pass space-separated command line arguments
(snakemake) as comma-separated to mrtrix

dbsc/config/snakebids.yml

@@ -114,7 +114,7 @@ parse_args:
 
   --shells:
     help: '(Mrtrix3) specify one or more b-values to use during processing, as
-          a comma-separated list of the desired approximate b-values (b-values
+          a space-separated list of the desired approximate b-values (b-values
           are clustered to allow for small deviations). Note that some
           commands are incompatible with multiple b-values, and will report an
           error if more than one b-value is provided.
@@ -128,7 +128,7 @@ parse_args:
   --lmax:
     help: '(Mrtrix3) the maximum spherical harmonic order for the output
           FOD(s). For algorithms with multiple outputs, this should be
-          provided as a comma-sperated list of integers, one for each output
+          provided as a space-sperated list of integers, one for each output
           image; for single-output algorithms, only a single integer
           should be provided. If omitted, commands will use the lmax of the
           corresponding response function (i.e. based on its number of

dbsc/workflow/rules/mrtpipelines.smk

@@ -130,8 +130,8 @@ rule dwi2response:
         dwi=rules.nii2mif.output.dwi,
         mask=rules.nii2mif.output.mask,
     params:
-        shells=f"-shells {shells}" if shells else "",
-        lmax=f"-lmax {lmax}" if lmax else "",
+        shells=f"-shells {','.join(shells)}" if shells else "",
+        lmax=f"-lmax {','.join(lmax)}" if lmax else "",
     output:
         wm_rf=bids_response_out(
             desc="wm",
@@ -222,7 +222,7 @@ rule dwi2fod:
             )
         ),
     params:
-        shells=f"-shells {shells}" if shells else "",
+        shells=f"-shells {','.join(shells)}" if shells else "",
     output:
         wm_fod=bids_response_out(
             model="csd",