rf: move working directory default to parsing logic, display defaults in docs

Author: mgxd

docs/usage.rst

@@ -35,7 +35,6 @@ Command-Line Arguments
 .. argparse::
    :ref: fmriprep.cli.parser._build_parser
    :prog: fmriprep
-   :nodefault:
    :nodefaultconst:
 
 
@@ -45,7 +44,6 @@ The command-line interface of the docker wrapper
 .. argparse::
    :ref: fmriprep_docker.__main__.get_parser
    :prog: fmriprep-docker
-   :nodefault:
    :nodefaultconst:
 
 

fmriprep/cli/parser.py

@@ -691,7 +691,6 @@ def _fallback_trt(value, parser):
         '--work-dir',
         action='store',
         type=Path,
-        default=Path('work').absolute(),
         help='Path where intermediate results should be stored',
     )
     g_other.add_argument(
@@ -785,6 +784,9 @@ def parse_args(args=None, namespace=None):
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts), init=['nipype'])
 
+    if config.execution.work_dir is None:
+        config.execution.work_dir = Path('work').absolute()
+
     # Consistency checks
     force_set = set(config.workflow.force)
     ignore_set = set(config.workflow.ignore)