Commit 30a197ca authored by mmassaviol's avatar mmassaviol
Browse files

Add stop_cases and make raw_input general

parent bd1cc4c8
......@@ -39,6 +39,8 @@ def generate(name):
result += "PREPARE_REPORT_SCRIPTS = config[\"prepare_report_scripts\"]\n"
result += "OUTPUTS = config[\"outputs\"]\n"
result += "PARAMS_INFO = config[\"params_info\"]\n"
if ("stop_cases" in yaml.keys()):
result += "STOP_CASES = config[\"stop_cases\"]\n"
result += "config = config[\"params\"]\n"
result += "\n"
......@@ -84,14 +86,10 @@ def generate(name):
result += "\tinputs = dict()\n"
if "params" in step:
for param in step["params"]:
if param["origin_command"] == "raw_reads":
result += "\tinputs[\"" + param["input_name"] + "\"] = raw_reads[\""+param["origin_name"]+"\"]\n"
if "raw_" in param["origin_command"] :
result += "\tinputs[\"" + param["input_name"] + "\"] = "+param["origin_command"]+"[\""+param["origin_name"]+"\"]\n"
else:
result += "\tinputs[\"" + param["input_name"] + "\"] = rules." + param["origin_command"] + ".output." + param["origin_name"] + "\n"
result += "\treturn inputs\n"
......
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