Hi! When running baqlava with bacterial read depletion, would it be possible to include the --metaphlan-options flag from humann3.9? This might make it easier to get around issues with the humann config file, as well as allow users to create different parallel runs with custom bacterial databases. Alternatively, is there a way to manually edit the baqlava scripts to hardcode this flag into the baqlava pipeline?
E.g.
baqlava -i baqlava/examples/baqlava_demo.fq -o <PATH/TO/OUTPUT> --nucdb examples/BAQLaVa.V0.5.nucleotide/ --protdb examples/BAQLaVa.V0.5.protein/ --metaphlan-options "--bowtie2db /home/user/databases/metaphlan/vJun23/ -x mpa_vJun23_CHOCOPhlAnSGB_202307"
Thanks so much!