bug fixed: nextflow.config now also correct if processes are not started in virtual environment

psot/nextflow.py

@@ -255,11 +255,6 @@ def generate_nextflow_config(execution):
             config['container'] = "container = " + "'" + m['analysis']['container'] + "'"
         else:
             config['container'] = ''
-            
-        if 'venv' in execution:
-            config['beforeScript'] = "beforeScript = 'export PS1=; source " + execution['venv'] + "/bin/activate'"
-        else:
-            config['beforeScript'] = ''
 
         if execution['use_cluster']:
             config['executor'] = 'sge'
@@ -267,13 +262,20 @@ def generate_nextflow_config(execution):
         else:
             config['executor'] = 'local'
             config['clusterOptions'] = ''
-
-        fragments.append(analysis_config_template.substitute(config))
-        if execution['fetch_informations']:
-            config['process_names'] = "'" + Template('convert_${id}_to_json|retrieve_informations_for_${id}').substitute(config) + "'"
+        
+        if 'venv' in execution:
+            config['beforeScript'] = "beforeScript = 'export PS1=; source " + execution['venv'] + "/bin/activate'"
+            
+            if execution['fetch_informations']:
+                config['process_names'] = "'" + Template('convert_${id}_to_json|retrieve_informations_for_${id}').substitute(config) + "'"
+            else:
+                config['process_names'] = Template('convert_${id}_to_json').substitute(config)
+                
+            fragments.append(analysis_config_template.substitute(config))
+            fragments.append(beforeScript_config_template.substitute(config))
         else:
-            config['process_names'] = Template('convert_${id}_to_json').substitute(config)
-        fragments.append(beforeScript_config_template.substitute(config))
+            config['beforeScript'] = ''
+            fragments.append(analysis_config_template.substitute(config))
         
     fragments.append('''}''')