Debug case with no SeOrPe param

generate_multiqc_config.py

 import re
 import sys
-from tools import *
+from tools import read_yaml
 
 config = read_yaml(sys.argv[1])
 
@@ -21,7 +21,7 @@ def report_section_order():
             res += "    " + "order: " + str(cpt) + "\n"
             cpt += -10
         for rule in config["outputs"][tool]:
-            if ((config["params"]["SeOrPe"] == "SE" and not("_PE" in rule)) or (config["params"]["SeOrPe"] == "PE" and not("_SE" in rule))):
+            if ("SeOrPe" not in config.keys() or (config["params"]["SeOrPe"] == "SE" and not("_PE" in rule)) or (config["params"]["SeOrPe"] == "PE" and not("_SE" in rule))):
                 for output in config["outputs"][tool][rule]:
                     if("file" in output.keys() and "mqc" in output["file"] and '{' not in output["file"]): # case of dynamic files ({wildcard}_mqc.png) to deal with
                         section = re.sub('\_mqc.*$', '', output["file"])

workflows/global_rules.snakefile

@@ -27,7 +27,7 @@ rule prepare_report:
                 tool = config[step["name"]]
                 i=1
                 for command in OUTPUTS[tool]:
-                    if ((config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
+                    if ("SeOrPe" not in config.keys() or (config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
                         outputs = OUTPUTS[tool][command]
                         for files in outputs:
                             name = files["file"] if 'file' in files.keys() else files["directory"]
@@ -43,7 +43,7 @@ rule prepare_report:
         for step in STEPS:
             tool = config[step["name"]]
             for key, value in config.items():    
-                if (tool in key and tool != "null") or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ((config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
+                if (tool in key and tool != "null") or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ("SeOrPe" not in config.keys() or (config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
                     if (key in PARAMS_INFO.keys() and "label" in PARAMS_INFO[key].keys()):
                         description = PARAMS_INFO[key]["label"]
                     else: