Defer the creation of the funnel job

modules/Bio/EnsEMBL/Hive/Analysis.pm

@@ -391,16 +391,11 @@ sub dataflow {
                 die "Asked to dataflow into $funnel_job_count funnel jobs instead of 1";
 
             } else {
-                my $funnel_job = Bio::EnsEMBL::Hive::AnalysisJob->new(
-                    @$common_params,
-                    'input_id'          => $output_ids_for_this_rule->[0],
-                    'status'            => 'SEMAPHORED',
-                );
 
                     # NB: $job_adaptor happens to belong to the $funnel_job, but not necesarily to $fan_jobs or $emitting_job
-                my ($semaphore_id, $funnel_job_id, @fan_job_ids) = $job_adaptor->store_a_semaphored_group_of_jobs( $funnel_job, $fan_jobs, $emitting_job );
+                my ($semaphore_id, @fan_job_ids) = $job_adaptor->store_a_semaphored_group_of_jobs( $output_ids_for_this_rule->[0], $fan_jobs, $emitting_job );
 
-                push @output_job_ids, $funnel_job_id, @fan_job_ids;
+                push @output_job_ids, @fan_job_ids;
             }
         } else {    # non-semaphored dataflow (but potentially propagating any existing semaphores)
             my @non_semaphored_jobs = map { Bio::EnsEMBL::Hive::AnalysisJob->new(

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -238,7 +238,7 @@ sub store_jobs_and_adjust_counters {
 =cut
 
 sub store_a_semaphored_group_of_jobs {
-    my ($self, $funnel_job, $fan_jobs, $emitting_job, $no_leeching) = @_;
+    my ($self, $funnel_input_id, $fan_jobs, $emitting_job, $no_leeching, $dependent_dataflow_rule) = @_;
 
     my $emitting_job_id;
 
@@ -317,7 +317,7 @@ sub store_a_semaphored_group_of_jobs {
 
     my (@fan_job_ids) = @{ $self->store_jobs_and_adjust_counters( $fan_jobs, 1, $emitting_job_id) };
 
-    return ($funnel_semaphore->dbID, $funnel_job_id, @fan_job_ids);
+    return ($funnel_semaphore->dbID, @fan_job_ids);
 }
 
 

scripts/seed_pipeline.pl

@@ -135,8 +135,7 @@ sub main {
     my ($semaphore_id, $job_id);
 
     if( $wrap_in_semaphore ) {
-        my $dummy;
-        ($semaphore_id, $dummy, $job_id) = $job_adaptor->store_a_semaphored_group_of_jobs( undef, [ $job ], undef );
+        ($semaphore_id, $job_id) = $job_adaptor->store_a_semaphored_group_of_jobs( undef, [ $job ], undef );
     } else {
         ($job_id) = @{ $job_adaptor->store_jobs_and_adjust_counters( [ $job ] ) };
     }