Provide typical usage of --tools

[ameynert]

Description of feature

The regex for describing how to specify --tools is not easy to understand for non-command line users. Adding some tool combination examples for typical usage would be helpful. Also suggest specifying the exact capitalization for each tool with the tool listing, not just in the regex.

[FriederikeHanssen]

so something like

example usage:

--tools strelka,snpeff

?

[ameynert]

Yes, just like that. Some starting point recommendations for e.g. germline vs tumour/normal, WGS or exome would also be useful.

[FriederikeHanssen]

https://nf-co.re/sarek/3.0.2/usage#which-variant-calling-tool-is-implemented-for-which-data-type we have this table, is this sufficient? We could add a link to the help output of the parameter section. I am a bit hesitant of explicitely recommending a tool without knowing the use case tbh.

[ameynert]

How about linking to that from the help for --tools?

[FriederikeHanssen]

:D hah yes just updated my comment. sounds like a good idea 👍

[asp8200]

Hmmm 🤔 So on the abovementioned table strelka is called "Strelka2", but one is suppose to write --tools strelka on the command line?

Similarly, the command for "GATK Haplotypecaller" is --tools haplotypecaller.

Moreover, it is not clear to me whether one needs to use the capitalization of the names of the tools on the command line as it is done on in the table, that is, the table lists, for instance, FreeBayes but should one write --tools FreeBayes on the command line? (I happen to know that --tools freebayes will work, but will --tools FreeBayes also work?)

[maxulysse]

we should really fix #892, that will help with the spelling of the tools