Quick edits to speed up Circle CI tests

[cansavvy]

Purpose/implementation

CircleCI tests take ~11 min in part due to some of the snv caller tests and largeness of the VarDict file (even when it is subset).

Vaf filter has been upped from 0.10 to 0.25, this should cut down the VarDict file some more and speed up some of the analysis steps.

Issue

NA

Results

NA

Docker and continuous integration

• This analysis has been added to continuous integration.

[jaclyn-taroni]

This still takes over 8 minutes. Is there anything you think you would not be thoroughly testing if you raised the cutoff further?

[jashapiro]

One other speedup that seems worth doing... hg38_genomic_region_annotation.rds is not too big for github, and generating it takes a good couple minutes every time. It's only 40MB, and won't change often, so it seems reasonable to include it in the repo. Thoughts?

[cansavvy]

That sounds good, @jashapiro I will do that change.

[jaclyn-taroni]

I would still try increasing the cutoff further, unless that would prevent something from being tested.

[cansavvy]

I would still try increasing the cutoff further, unless that would prevent something from being tested.

I've upped it to 0.5.

Another way to decrease the run time for snv caller bit is to turn off the regional analysis which I made an option for on another branch. Although I think it is a good analysis to do, I think it would be better to do it after we reach a consensus. The results of that analysis haven't added to the consensus mutation decisions. Thoughts?

[jaclyn-taroni]

You're referencing #159 (comment) correct? Let's have that discussion over there.

[jaclyn-taroni]

⚡️

[jaclyn-taroni]

Was removing wxs_bed_regions_all.tsv intentional?

[cansavvy]

Was removing wxs_bed_regions_all.tsv intentional?

Yes it is an old development remnant that was a place holder before v5 data was released and had the actual BED regions files. It should be removed.