Fix shells and lmax argurments #39
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Do you mind merging from main so the linters work properly? |
- adds necessary changes to pass space-separated command line arguments (snakemake) as comma-separated to mrtrix
kaitj
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Rebased from main, workflows should work now. |
tkkuehn
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Jan 26, 2023
| @@ -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 | |||
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Unrelated to the changes at hand but while I'm looking at this, if --lmax can be ommitted, nargs should be "*".
| @@ -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 "", | |||
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Loking at the help text (and nargs) of the --shells argument, it needs to be there, right? Maybe worth erroring out/raising an exception somewhere if this isn't defined.
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Doesn't have to be required (similar to lmax).
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Proposed changes
Resolves #34.
Fixes the arguments to pass space-separated command line arguments (snakemake) as comma-separated to mrtrix rules (as necessary)
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