update bbtools version and parameters

[aclum]

JGI is on bbtools 39.03

Alicia to confirm final parameters with Brian.

cc @kaijli

[ssarrafan]

Sprint over, removing from sprint.

[kaijli]

@aclum is it confirmed? is there a specific docker image for that?

[aclum]

I'll finalize this next week. There were some recommendations for removing optical duplicates that I need to review.

[aclum]

The instrument name in the schema currently is a string field so we can't automate removal of optical duplicates settings. We'll revisit this once Berkeley schema is out in ~October.

@kaijli Please update the bbtools container 39.03.

[kaijli]

bumped bbtools ver.
successful run at jaws id 79956
dd222dc

[ssarrafan]

Will move to next sprint for review
@aclum @kaijli

[aclum]

Over slack based on a conversation with Brian we decided to also add extend=f, this was being turned on behind the scenes which was enabling tadpole and using up large amounts of memory.
If we enable extend=t we should be able to reduce the memory for the rqc filter task to 115 Gb, leave threads at 64 and CPU at 32.

[kaijli]

successful run with added extend=f and lowered memory at jaws id 80306

[aclum]

Looks great. Last thing is we need to add verifypaired=t to stage_interleave

[kaijli]

17ffa95 done, successful run on expanse

[ssarrafan]

@kaijli @aclum based on the last comment from Kaitlyn assuming this is done.