MAIN: tidy workflow

[eilidhmacnicol]

Overhaul of the workflow section to reduce unnecessary repeats of code. Fixed code now allows artsBrainExtraction to run from the command line without errors.

Requires #22 to be merged first since this includes changes from that branch.

[pull-assistant]

Best reviewed: commit by commit

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Optimal code review plan

     MAIN: workflow tidying

     FIX: correct TemplateFlow mask call

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[oesteban]

A quick first pass

[pep8speaks]

Hello @eilidhmacnicol! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file nirodents/workflows/brainextraction.py:

Line 65:100: E501 line too long (111 > 99 characters)
Line 199:5: E265 block comment should start with '# '
Line 200:5: E265 block comment should start with '# '
Line 233:5: E265 block comment should start with '# '
Line 259:9: E265 block comment should start with '# '
Line 279:9: E265 block comment should start with '# '
Line 284:9: E265 block comment should start with '# '