X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=c3b5f0af58ab6ef0627a6a42784c76c2813184bf;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=ca832314d66dbe371e314db292ab6f441d2ee351;hpb=957d67f7d8bbadfd2930de061e89fd9b149270fd;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index ca83231..c3b5f0a 100644
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -140,6 +140,8 @@ int GetCurrentCommand::execute(){
 					m->setFlowFile("");
                 }else if (types[i] == "biom") {
 					m->setBiomFile("");
+                }else if (types[i] == "counttable") {
+					m->setCountTableFile("");
 				}else if (types[i] == "processors") {
 					m->setProcessors("1");
 				}else if (types[i] == "all") {