Skip to content

Make --recon-spec a required argument #375

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
tsalo merged 1 commit into from
Apr 15, 2026
+7 −3
Merged

Make --recon-spec a required argument #375

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 7 additions & 3 deletions qsirecon/cli/parser.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -337,7 +337,8 @@ def _bids_filter(value, parser):
'--recon-spec',
action='store',
type=str,
help='json file specifying a reconstruction pipeline to be run after preprocessing',
help='YAML file specifying a reconstruction pipeline to be run.',
required=True,
)
g_recon.add_argument(
'--input-type',
Expand Down Expand Up @@ -422,8 +423,11 @@ def _bids_filter(value, parser):
'--config-file',
action='store',
metavar='FILE',
help='Use pre-generated configuration file. Values in file will be overridden '
'by command-line arguments.',
help=(
'Use pre-generated configuration file. Values in file will be overridden '
'by command-line arguments. '
'This is not currently used by QSIRecon.'
),
)
g_other.add_argument(
'--write-graph',
Expand Down