Run wf

gga_run_workflow_phaeo_jbrowse.py

@@ -583,10 +583,12 @@ if __name__ == "__main__":
                     species_strain_sex=species_strain_sex_org2,
                     id="{id}")
                 # Replace values in the workflow dictionary
-                jbrowse_tool_state_org1 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]
-                jbrowse_tool_state_org1 = jbrowse_tool_state_org1.replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
-                jbrowse_tool_state_org2 = workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]
-                jbrowse_tool_state_org2 = jbrowse_tool_state_org2.replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"]\
+                    .replace("__MENU_URL_ORG1__", jbrowse_menu_url_org1)
+                workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"] = \
+                    workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JRBOWSE_ORG2]["tool_state"]\
+                    .replace("__MENU_URL_ORG2__", jbrowse_menu_url_org2)
                 # The UNIQUE_ID is specific to a combination genus_species_strain_sex so every combination should have its unique workflow
                 # in galaxy --> define a naming method for these workflows
                 workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER]["tool_state"] = \