diff --git a/src/dsc_translator.py b/src/dsc_translator.py
index f513f980..72fbebe7 100644
--- a/src/dsc_translator.py
+++ b/src/dsc_translator.py
@@ -74,7 +74,7 @@ def __init__(self, workflows, runtime, rerun = False, n_cpu = 4, try_catch = Fal
                     processed_steps[(step.name, flow, depend)] = name
                     if not step.name in self.depends:
                         self.depends[step.name] = []
-                    if step.depends not in self.depends[step.name]:
+                    if len(step.depends) and step.depends not in self.depends[step.name]:
                         self.depends[step.name].append(step.depends)
                     conf_translator = self.Step_Translator(step, self.db,
                                                            self.step_map[workflow_id + 1],
@@ -110,7 +110,7 @@ def __init__(self, workflows, runtime, rerun = False, n_cpu = 4, try_catch = Fal
                     tmp_str.append(f"depends: [sos_step('%s_%s' % (n2a(x[1]).lower(), x[0])) for x in IO_DB['{workflow_id + 1}']['{y}']['depends']]")
                 tmp_str.append(f"output: IO_DB['{workflow_id + 1}']['{y}']['output']")
                 tmp_str.append(f"sos_run('{y}', {y}_output_files = IO_DB['{workflow_id + 1}']['{y}']['output'], " + \
-                               (f"{y}_input_files = IO_DB['{workflow_id + 1}']['{y}']['input'], " if self.depends[y] else "") + \
+                               (f"{y}_input_files = IO_DB['{workflow_id + 1}']['{y}']['input'], " if len(self.depends[y]) else "") + \
                                f"DSC_STEP_ID_ = {abs(int(xxh(repr(exe_signatures[y])).hexdigest(), 16)) % (10**8)})")
                 if ii == len(sequence):
                     self.last_steps.append((y, workflow_id + 1))
diff --git a/src/query_engine.py b/src/query_engine.py
index 0269812a..27b633d5 100644
--- a/src/query_engine.py
+++ b/src/query_engine.py
@@ -267,22 +267,13 @@ def get_sequence(primary, reference):
                     raise ValueError(f'Requested module ``{primary[idx+1]}`` is an orphan branch. Please consider using separate queries for information from this module.')
             return primary
         #
-        pipelines = []
-        tables = case_insensitive_uniq_list([x[0] for x in self.target_tables] + [x[0] for x in self.condition_tables])
-        for pipeline in self.pipelines:
-            pidx = [l[0] for l in enumerate(pipeline) if l[1] in tables]
-            if len(pidx) == 0:
-                continue
-            pidx = [0] + pidx
-            if not pipeline[pidx[0]:pidx[-1]+1] in pipelines:
-                pipelines.append(pipeline[pidx[0]:pidx[-1]+1])
-        pipelines = filter_sublist(pipelines)
-        # remove tables in targets not exist in pipelines
+        valid_tables = [[item[0] for item in self.target_tables + self.condition_tables if item[0] in pipeline] for pipeline in self.pipelines]
+        # 1. Further filter pipelines to minimally match target table dependencies
+        # 2. For pipelines containing each other we only keep the longest pipelines
+        pipelines = filter_sublist([get_sequence(tables, pipeline) for tables, pipeline in zip(valid_tables, self.pipelines)])
         target_tables = [[item for item in self.target_tables if item[0] in pipeline] for pipeline in pipelines]
-        non_empty_targets = [idx for idx, item in enumerate(target_tables) if len(item)>0]
-        # now the pipelines needs be further filtered to match target table dependencies
-        pipelines = [get_sequence([x[0] for x in tables], pipeline) for tables, pipeline in zip(target_tables, pipelines)]
         condition_tables = [[item for item in self.condition_tables if item[0] in pipeline] for pipeline in pipelines]
+        non_empty_targets = [idx for idx, item in enumerate(target_tables) if len(item) > 0]
         return [pipelines[i] for i in non_empty_targets], [target_tables[i] for i in non_empty_targets], [condition_tables[i] for i in non_empty_targets]
 
     def get_from_clause(self):