sffFile = validParameter.validFile(parameters, "sff", true);
if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
else if (sffFile == "not open") { sffFile = ""; abort = true; }
+ else { m->setSFFFile(sffFile); }
oligosFile = validParameter.validFile(parameters, "oligos", true);
if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }