X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;fp=pipelinepdscommand.cpp;h=898ad9b72640a4f5c9050f98b399e23efeafd58d;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=7a9d53089cd1b59b7fd278936c28e3f231bea005;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 7a9d530..898ad9b 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -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;  }