Error when running RNAnue without control sample

[riasc]

Hi @ChristopherAdelmann,

I found the following issue when control data is not provided --ctrls = (left empty in the config file). The preproc works but when applying the following steps like align this reports the following errors:

[2024-06-27 10:28:30] ctrls: "/data/results_20160829/preproc/ctrls" [2024-06-27 10:28:30] ### ERROR - "/data/results_20160829/preproc/ctrls" has not been found in the filesystem!

The reason for that is that in Data.cpp the ctrls and trtms fields are just forwarded to the GetGroupsPath function.

RNAnue/src/Data.cpp

Lines 37 to 38 in 995cb80

	GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);
	getCondition(groups);

So you might want to include a check for all the steps to make sure that --ctrls in provided.. like so?

  fs::path ctrlsPath = "";
  if(params["ctrls"].as<std::string>() != "") {
      ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
  }
  fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/trtms";

Also when substituting:

RNAnue/src/Data.cpp

Lines 136 to 137 in 995cb80

	std::cout << helper::getTime() << "### ERROR - " << group.second << " has not been found in the filesystem!\n";
	exit(EXIT_FAILURE);

with:

std::cout << "has not been found in the filesystem! ### ERROR ### \n";

The output should appear a bit nicer... e.g.,

[2024-06-27 10:28:30] ctrls: "/data/results_20160829/preproc/ctrls" has not been found in the filesystem! ### ERROR ###