it->second = m->getDesignFile();
}else if (it->first == "sff") {
it->second = m->getSFFFile();
+ }else if (it->first == "flow") {
+ it->second = m->getFlowFile();
}else if (it->first == "oligos") {
it->second = m->getOligosFile();
}else if (it->first == "accnos") {
it->second = m->getTaxonomyFile();
}else if (it->first == "biom") {
it->second = m->getBiomFile();
- }else if (it->first == "counttable") {
+ }else if (it->first == "count") {
it->second = m->getCountTableFile();
+ }else if (it->first == "summary") {
+ it->second = m->getSummaryFile();
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
}