Jobs with totally-failed successors will not wait for other successors to finish as intended
This line in leader.py is broken and I'm pretty sure it will never evaluate to true:
https://github.com/BD2KGenomics/toil/blob/1195effda167eea9d1d623f2de0794c138de75b9/src/toil/leader.py#L756

The `toilState.successorCounts` dict is keyed by JobWrappers, not jobStoreIDs.

(The `__hash__` method of JobWrapper gives the same hash as its jobStoreID, but that only determines its bucket in the dict. `__eq__` is still used to compare items with the same hash value.)

I think the only side effect is that jobs with totally failed successors will terminate early as totally failed, rather than waiting for the successors to finish.

The fix should be trivial, let me know if you want it as a PR or to fix on your own.

diff --git a/src/toil/leader.py b/src/toil/leader.py
index 8bf77545..1c2a1993 100644
--- a/src/toil/leader.py
+++ b/src/toil/leader.py
@@ -362,10 +362,10 @@ class JobBatcher:
 
         else:
             for predecessorJob in self.toilState.successorJobStoreIDToPredecessorJobs.pop(jobStoreID):
-                self.toilState.successorCounts[predecessorJob] -= 1
-                assert self.toilState.successorCounts[predecessorJob] >= 0
-                if self.toilState.successorCounts[predecessorJob] == 0: #Job is done
-                    self.toilState.successorCounts.pop(predecessorJob)
+                self.toilState.successorCounts[predecessorJob.jobStoreID] -= 1
+                assert self.toilState.successorCounts[predecessorJob.jobStoreID] >= 0
+                if self.toilState.successorCounts[predecessorJob.jobStoreID] == 0: #Job is done
+                    self.toilState.successorCounts.pop(predecessorJob.jobStoreID)
                     logger.debug('Job %s has all its non-service successors completed or totally '
                                  'failed', predecessorJob.jobStoreID)
                     assert predecessorJob not in self.toilState.updatedJobs
@@ -385,7 +385,8 @@ class ToilState( object ):
     def __init__( self, jobStore, rootJob, jobCache=None):
         # This is a hash of jobs, referenced by jobStoreID, to their predecessor jobs.
         self.successorJobStoreIDToPredecessorJobs = { }
-        # Hash of jobs to counts of numbers of successors issued.
+        
+        # Hash of jobStoreIDs to counts of numbers of successors issued.
         # There are no entries for jobs
         # without successors in this map.
         self.successorCounts = { }
@@ -400,11 +401,14 @@ class ToilState( object ):
 
         # Jobs (as jobStoreIDs) with successors that have totally failed
         self.hasFailedSuccessors = set()
+        
         # Jobs that are ready to be processed
         self.updatedJobs = set( )
+        
         # The set of totally failed jobs - this needs to be filtered at the
         # end to remove jobs that were removed by checkpoints
         self.totalFailedJobs = set()
+        
         ##Algorithm to build this information
         logger.info("(Re)building internal scheduler state")
         self._buildToilState(rootJob, jobStore, jobCache)
@@ -444,7 +448,7 @@ class ToilState( object ):
                 jobWrapper.command = jobWrapper.checkpoint
 
         else: # There exist successors
-            self.successorCounts[jobWrapper] = len(jobWrapper.stack[-1])
+            self.successorCounts[jobWrapper.jobStoreID] = len(jobWrapper.stack[-1])
             for successorJobStoreTuple in jobWrapper.stack[-1]:
                 successorJobStoreID = successorJobStoreTuple[0]
                 if successorJobStoreID not in self.successorJobStoreIDToPredecessorJobs:
@@ -812,8 +816,8 @@ def innerLoop(jobStore, config, batchSystem, toilState, jobBatcher, serviceManag
                                  jobWrapper.jobStoreID, len(jobWrapper.stack[-1]))
                     #Record the number of successors that must be completed before
                     #the jobWrapper can be considered again
-                    assert jobWrapper not in toilState.successorCounts
-                    toilState.successorCounts[jobWrapper] = len(jobWrapper.stack[-1])
+                    assert jobWrapper.jobStoreID not in toilState.successorCounts
+                    toilState.successorCounts[jobWrapper.jobStoreID] = len(jobWrapper.stack[-1])
                     #List of successors to schedule
                     successors = []
                     #For each successor schedule if all predecessors have been completed
['src/toil/leader.py']