# Adding a --metaphlan-options and/or bowtie2db flag to baqlava

**URL:** <https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455>\
**Category:** BAQLaVa\
**Created:** [August 28, 2025, 4:59pm UTC](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455 "2025-08-28T16:59:38Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jawah003](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jawah003/32/3230_2.png) [@jawah003](https://forum.biobakery.org/u/jawah003)\
**Post date:** [August 28, 2025, 4:59pm UTC](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455/1 "2025-08-28T16:59:38Z")

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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!

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**Author:** ![scottdaniel\_at\_chop](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/scottdaniel_at_chop/32/3505_2.png) [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\
**Post date:** [December 4, 2025, 4:28pm UTC](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455/2 "2025-12-04T16:28:07Z")

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Adding on to this, there should be an option to specify the location of the `humann` databases.

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**Author:** ![jjensen44](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jjensen44/32/3298_2.png) [@jjensen44](https://forum.biobakery.org/u/jjensen44)\
**Post date:** [December 4, 2025, 8:10pm UTC](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455/3 "2025-12-04T20:10:04Z")

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Hi @jawah003 and @scottdaniel_at_chop, thank you for the information on how users are interacting with BAQLaVa! It is useful to know that pass-through options to facilitate specifics of the HUMAnN run would be useful to you both.