sample_list_generator.sh needs to NOT be recursive (pull sample names from directories below the directory you give it). A lot of times people in our lab will move problem files or truncated files or whatever into directories like ~/project/Read_Mapping/Problem_Samples. When I go to make a sample list of the good samples that I want to continue with on to SAM_Processing, sample_list_generator.sh includes all the problem samples that I don't want. I have never once found the recursive nature of sample_list_generator.sh to be helpful, so I think it should probably just be removed.
sample_list_generator.sh needs to NOT be recursive (pull sample names from directories below the directory you give it). A lot of times people in our lab will move problem files or truncated files or whatever into directories like ~/project/Read_Mapping/Problem_Samples. When I go to make a sample list of the good samples that I want to continue with on to SAM_Processing, sample_list_generator.sh includes all the problem samples that I don't want. I have never once found the recursive nature of sample_list_generator.sh to be helpful, so I think it should probably just be removed.