ENH: Skip newline before Python call in batch submission to facilitate containerized runs (#3297)

* Avoid empty line in bash script output

Remove the newline at the end of template to avoid having am empty line after joining with the node command. This allows to have the node command integrated in more complex call, such as a `singularity exec ...` call.

* Rather remove the newlines than trim the last char of the template.

As per @effigies suggestion.

Co-authored-by: Chris Markiewicz <[email protected]>

Co-authored-by: Christopher J. Markiewicz <[email protected]>
Co-authored-by: Chris Markiewicz <[email protected]>

Author: d-vogel

nipype/pipeline/plugins/base.py

@@ -543,7 +543,9 @@ def _submit_job(self, node, updatehash=False):
         pyscript = create_pyscript(node, updatehash=updatehash)
         batch_dir, name = os.path.split(pyscript)
         name = ".".join(name.split(".")[:-1])
-        batchscript = "\n".join((self._template, "%s %s" % (sys.executable, pyscript)))
+        batchscript = "\n".join(
+            (self._template.rstrip("\n"), "%s %s" % (sys.executable, pyscript))
+        )
         batchscriptfile = os.path.join(batch_dir, "batchscript_%s.sh" % name)
         with open(batchscriptfile, "wt") as fp:
             fp.writelines(batchscript)