X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=968ba4f66a9d233a14e5f579e9563ac4d9bbd706;hb=cbaa068e77aeb15bb06f0695a36d8f757977ed64;hp=7a9d53089cd1b59b7fd278936c28e3f231bea005;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 7a9d530..968ba4f 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -180,7 +180,7 @@ PipelineCommand::PipelineCommand(string option) {
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			if (pipeFilename != "") {
 				abort = readUsersPipeline();
@@ -188,6 +188,7 @@ PipelineCommand::PipelineCommand(string option) {
 				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;  }