enh: allow node specific plugin args for sge and pbs

Author: satra

nipype/pipeline/engine.py

@@ -973,6 +973,7 @@ def __init__(self, interface, iterables=None, overwrite=None,
         self.run_without_submitting = run_without_submitting
         self.input_source = {}
         self.needed_outputs = []
+        self.plugin_args = {}
         if needed_outputs:
             self.needed_outputs = sorted(needed_outputs)
 

nipype/pipeline/plugins/pbs.py

@@ -52,6 +52,12 @@ def _submit_batchtask(self, scriptfile, node):
         qsubargs = ''
         if self._qsub_args:
             qsubargs = self._qsub_args
+        if 'qsub_args' in node.plugin_args:
+            if 'overwrite' in node.plugin_args and \
+               node.plugin_args['overwrite']:
+                qsubargs = node.plugin_args['qsub_args']
+            else:
+                qsubargs += (" " + node.plugin_args['qsub_args'])
         if '-o' not in qsubargs:
             qsubargs = '%s -o %s' % (qsubargs, path)
         if '-e' not in qsubargs:

nipype/pipeline/plugins/sge.py

@@ -53,6 +53,12 @@ def _submit_batchtask(self, scriptfile, node):
         qsubargs = ''
         if self._qsub_args:
             qsubargs = self._qsub_args
+        if 'qsub_args' in node.plugin_args:
+            if 'overwrite' in node.plugin_args and\
+               node.plugin_args['overwrite']:
+                qsubargs = node.plugin_args['qsub_args']
+            else:
+                qsubargs += (" " + node.plugin_args['qsub_args'])
         if '-o' not in qsubargs:
             qsubargs = '%s -o %s' % (qsubargs, path)
         if '-e' not in qsubargs: