create "recommended" option for requiredness in template.csv

[lwaldron]

Currently, only "required" or "optional" are permissible. Add "warning" as a possibility, and this will return a warning in the check and in the produced vignette.

[lwaldron]

@paolinomanghi @edoardopasolli where should there be a "warning" option in the template? If it is added we can use it.

[edoardopasolli]

I would put it in:
antibiotics_current_use
disease
study_condition
age_category
gender
country
non_westernized
These are "optional" fields, but I think a curator should be able to get them in most of the cases

[paolinomanghi]

I would use as a mandatory also - subject ID - the number of reads - the number of bases - the type of sequencing machine (not really the 2000/4000, just the type, as it is now) I'd rather not consider sex (gender) as mandatory because is not guaranteed to have it (some modern policies prefer not to deploy it, see the latest Zeharnakova paper), also when other nice metadata are available. Instead, for example, age_category is almost alwasy retrievable looking into the paper.

…

On Mon, Jan 4, 2021 at 5:06 PM edoardopasolli ***@***.***> wrote: I would put it in: antibiotics_current_use disease study_condition age_category gender country non_westernized These are "optional" fields, but I think a curator should be able to get them in most of the cases — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGZXSV6MQWNUNT77AKQRMIDSYHRRHANCNFSM4EBPGEVQ> .

[lwaldron]

Call this "recommended" instead.