When running quality trimming on paired-end samples, the SINGLES_ADAPTED variable in the config file must be set to a dummy value, or the script bugs out. This should be changed so that paired-end samples can be run even when this is left blank.
I suspect this same issue exists in reverse for single-end samples, but that's an issue for another day.
Reminder to myself to fix this later.
When running quality trimming on paired-end samples, the SINGLES_ADAPTED variable in the config file must be set to a dummy value, or the script bugs out. This should be changed so that paired-end samples can be run even when this is left blank.
I suspect this same issue exists in reverse for single-end samples, but that's an issue for another day.