solve wait_for issue

run_template_construction.py

@@ -416,6 +416,7 @@ def applyWarpWrapper(img_path, ref_path, warped_path, warp_path, interp='spline'
         applywarp(src=img_nib, ref=ref_path, out=warped_path, warp=warp_path, interp=interp)
 
 
+# https://git.fmrib.ox.ac.uk/fsl/fsl_sub
 # def submitJob_fsl_sub(name, log_dir, queue, wait_for=[], script=None, command=None, coprocessor_class=None, export_var=None,
 #                   debug=False):
 #     """! Wrapper for fslsub - submits a job to the cluster. This function can be easily extended to work with other workload managers.
@@ -492,14 +493,16 @@ def submitJob(name, log_dir, queue, wait_for=[], script=None, command=None, copr
 
     @return  The job ID.
     """
-    cmd = 'fsl_sub'
-    if wait_for and any(job != '' for job in wait_for):
+    cmd = 'fsl_sub -n'
+    job_ids_bool = [job != '' for job in wait_for]
+    if wait_for and any(job_ids_bool):
         cmd += ' -j '
-        for j, job in enumerate(wait_for):
-            if job != '':
-                cmd += job.replace("\n", "")
-                if j < len(wait_for) - 1:
-                    cmd += ','
+        wait_for_arr = np.array(wait_for)
+        wait_for_arr = wait_for_arr[job_ids_bool]
+        for j, job in enumerate(wait_for_arr):
+            cmd += job.replace("\n", "")
+            if j < len(wait_for_arr) - 1:
+                cmd += ','
 
     cmd += ' -N ' + name + \
            ' -l ' + log_dir + \
@@ -1383,10 +1386,9 @@ if __name__ == "__main__":
                         export_var_str[key] = '"' + key + '=' + ','.join([common_path]) + '"'
 
                 job_ids[28] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=gpuq,
-                                            wait_for=list(
-                                                itemgetter(*[21, 23, 24, 25, 26, 27, 28, 44, 45, 46, 47, 48, 50])(
-                                                    job_ids)), coprocessor_class='P',
-                                            export_var=export_var_str['SINGULARITY_BIND'], debug=False)
+                                        wait_for=list(itemgetter(*[21, 23, 24, 25, 26, 27, 28, 44, 45, 46, 47, 48, 50])(job_ids)),
+                                        coprocessor_class='P',
+                                        export_var=export_var_str['SINGULARITY_BIND'], debug=False)
                 print('submitted: ' + task_name)
 
 # Averaging warps