Why --vep_n_forks can't be 1?

[i-pletenev]

Dear PCGR/CPSR developers,

While running CPSR, I encountered an error:

"cpsr-validate-input-arguments-a - ERROR - Number of forks that VEP can use during annotation must be above 1 and not more than 8 (recommended is 4), current value is 1"

Indeed, looking at the code, it seems that vep_n_forks = 1 is not in the allowed range:

pcgr/pcgr/arg_checker.py

Lines 559 to 564 in 4b0408b

	if int(arg_dict['vep_n_forks']) <= int(pcgr_vars.VEP_MIN_FORKS) or \
	int(arg_dict['vep_n_forks']) > int(pcgr_vars.VEP_MAX_FORKS):
	err_msg = (
	f"Number of forks that VEP can use during annotation must be above {str(pcgr_vars.VEP_MIN_FORKS)} and not "
	f"more than {str(pcgr_vars.VEP_MAX_FORKS)} (recommended is 4), current value is {arg_dict['vep_n_forks']}"
	)

(VEP_MIN_FORKS = 1)

I am running many samples, each using a single cpu core. I was wondering if you could allow vep_n_forks = 1?

[sigven]

Hey @i-pletenev,

I'll have a check, don't think it should be a problem setting it to 1, even though it will likely slow things down (not completely sure why the lower limit is set to 2).

best,
Sigve

[sigven]

Just looked now, and I think running VEP by a single fork was intended to be allowed:
https://github.com/sigven/pcgr/blob/main/pcgr/pcgr_vars.py#L28

But there was a minor bug in the code here:
https://github.com/sigven/pcgr/blob/main/pcgr/arg_checker.py#L559 - I'll create a fix for this.

Thanks for reporting!

best,
Sigve

[i-pletenev]

Hey, @sigven! Great! Thank you for your time!