Commit 5776b361 by Alexandre Routier

Change order of the pipelines in the command line

parent 8f2168be
Pipeline #1084 failed with stages
in 4 seconds
......@@ -125,11 +125,11 @@ def execute():
from clinica.pipelines.t1_volume_new_template.t1_volume_new_template_cli import T1VolumeNewTemplateCLI # noqa
from clinica.pipelines.t1_volume_existing_template.t1_volume_existing_template_cli import T1VolumeExistingTemplateCLI #noqa
from clinica.pipelines.t1_volume_parcellation.t1_volume_parcellation_cli import T1VolumeParcellationCLI
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import DWIPreprocessingUsingT1CLI # noqa
from clinica.pipelines.dwi_preprocessing_noddi.dwi_preprocessing_noddi_cli import DwiPreprocessingNoddiCLI # noqa
from clinica.pipelines.dwi_processing_noddi.dwi_processing_noddi_cli import DwiProcessingNoddiCLI # noqa
from clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_cli import DWIPreprocessingUsingPhaseDiffFieldmapCLI # noqa
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import DWIPreprocessingUsingT1CLI # noqa
from clinica.pipelines.dwi_processing_dti.dwi_processing_dti_cli import DWIProcessingDTICLI # noqa
from clinica.pipelines.dwi_processing_noddi.dwi_processing_noddi_cli import DwiProcessingNoddiCLI # noqa
from clinica.pipelines.fmri_preprocessing.fmri_preprocessing_cli import fMRIPreprocessingCLI # noqa
from clinica.pipelines.pet_volume.pet_volume_cli import PETVolumeCLI # noqa
from clinica.pipelines.pet_surface.pet_surface_cli import PetSurfaceCLI # noqa
......
......@@ -26,7 +26,7 @@ class DwiPreprocessingNoddiCLI(ce.CmdParser):
def define_description(self):
"""Define a description of this pipeline.
"""
self._description = 'Preprocessing of raw DWI datasets with multi-shell acquisitions and phase encoding directions: http://clinica.run/doc/Pipelines/DWI_Preprocessing/'
self._description = 'Preprocessing of raw DWI datasets with multi-shell acquisitions and opposite phase encoding directions: http://clinica.run/doc/Pipelines/DWI_Preprocessing/'
def define_options(self):
"""Define the sub-command arguments
......@@ -80,7 +80,6 @@ class DwiPreprocessingNoddiCLI(ce.CmdParser):
create_subs_sess_list(args.bids_directory, temp_dir)
args.subjects_sessions_tsv = os.path.join(temp_dir, 'subjects_sessions_list.tsv')
#Run the DWIPreprocessingNoddi Pipeline from command line
pipeline = DwiPreprocessingNoddi(
bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
......@@ -102,4 +101,4 @@ class DwiPreprocessingNoddiCLI(ce.CmdParser):
elif args.slurm:
pipeline.run(plugin='SLURM')
else:
pipeline.run()
\ No newline at end of file
pipeline.run()
{
"id": "aramislab/dwi_preprocessing_noddi",
"id": "aramislab/dwi_preprocessing_multi_shell",
"author": "John Doe",
"version": "0.1.0",
"dependencies": [
......@@ -9,4 +9,4 @@
"version": ">=0.1.0"
}
]
}
\ No newline at end of file
}
......@@ -81,7 +81,5 @@ class DwiProcessingNoddiCLI(ce.CmdParser):
pipeline.base_dir = self.absolute_path(args.working_directory)
if args.n_procs:
pipeline.run(plugin='MultiProc', plugin_args={'n_procs': args.n_procs})
elif args.slurm:
pipeline.run(plugin='SLURM')
else:
pipeline.run()
\ No newline at end of file
pipeline.run()
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