address @effigies' comments

Author: oesteban

fmriprep/cli/run.py

@@ -607,7 +607,7 @@ def build_workflow(opts, retval):
 
     # First check that bids_dir looks like a BIDS folder
     bids_dir = os.path.abspath(opts.bids_dir)
-    layout = BIDSLayout(bids_dir, validate=False)
+    layout = BIDSLayout(bids_dir, validate=not opts.skip_bids_validation)
     subject_list = collect_participants(
         layout, participant_label=opts.participant_label)
 

fmriprep/workflows/base.py

@@ -425,8 +425,7 @@ def init_single_subject_wf(layout, subject_id, task_id, echo_idx, name, reportle
                       name='bidssrc')
 
     bids_info = pe.Node(BIDSInfo(
-        bids_dir=layout.root, bids_validate=False),
-        name='bids_info', run_without_submitting=True)
+        bids_dir=layout.root, bids_validate=False), name='bids_info')
 
     summary = pe.Node(SubjectSummary(output_spaces=output_spaces, template=template),
                       name='summary', run_without_submitting=True)

fmriprep/workflows/fieldmap/phdiff.py

@@ -73,8 +73,7 @@ def _pick1st(inlist):
         return inlist[0]
 
     # Read phasediff echo times
-    meta = pe.Node(ReadSidecarJSON(bids_validate=False), name='meta',
-                   mem_gb=0.01, run_without_submitting=True)
+    meta = pe.Node(ReadSidecarJSON(bids_validate=False), name='meta', mem_gb=0.01)
 
     # Merge input magnitude images
     magmrg = pe.Node(IntraModalMerge(), name='magmrg')