It looks like iguide setup --skip_demultiplexing currently fails because the config object isn't available to get_sample_list, and then the Demulti_Dir path is rejected because it already exists (because of the check_existing call). I think if the config object is passed to get_sample_list and check_existing is removed (maybe not relevant since it should exist in this case?) it should be OK.
cnobles
commented
5 years ago
It looks like
iguide setup --skip_demultiplexingcurrently fails because the config object isn't available to get_sample_list, and then the Demulti_Dir path is rejected because it already exists (because of the check_existing call). I think if the config object is passed to get_sample_list and check_existing is removed (maybe not relevant since it should exist in this case?) it should be OK.