Explicitly set "--skip_bbsplit false" with "--bbsplit_fasta_list" to use BBSplit

[G-Sarah]

Description of feature

Hello, first, thanks for the fantastic pipeline!

Pretty much all's in the title. The default value of --skip_bbsplit is 1 whether or not a fasta list is passed or not. The pipeline clearly lists the --bbsplit_fasta_list (and --save_bbsplit_reads) parameters in the non-default ones but still skips the step since --skip_bbsplit doesn't switch to 0.

It might sound silly but I lost quite a bit of time by assuming this was the default behavior. Maybe it should be?

Have a nice day!

[drpatelh]

Hi @G-Sarah ! Hope you are well!

All --skip_* parameters will have priority over others in this instance so unless you set --skip_bbsplit false then you won't be able to run BBSplit e.g. in the main workflow. This means we can provide all of the other parameters e.g. --bbsplit_fasta_list list.txt --save_bbsplit_reads by default to the pipeline if required and only have to toggle the value of --skip_bbsplit when required.

I will add a note to the docs where I can and get back to you.

[drpatelh]

Closing for now but please feel free to re-open if I have missed something here :)

[G-Sarah]

Ok I did not think of it that way. I think it would benefit from being explicit in the doc, yes. I guess it'll be a point to address in the upcoming doc hackathon. ^^
Thanks for your answer!

[G-Sarah]

Hello, I'm trying to clarify some points in the docs for the nf-core hackathon, and notably this --skip-bbsplit thingie, but the Parameter docs page doesn't seem to be on Github. Am I doing something wrong @drpatelh ?

[drpatelh]

Hi @G-Sarah ! The parameter docs are embedded and rendered directly from the parameter schema e.g. here. You can edit these by using the nf-core schema build command in a cloned version of the repo. Some docs here. If they are going to be very extensive then maybe we put them in the docs/usage.md instead.

Let me know if you need anything else.

Thanks!

[G-Sarah]

Hi @G-Sarah ! The parameter docs are embedded and rendered directly from the parameter schema e.g. here. You can edit these by using the nf-core schema build command in a cloned version of the repo. Some docs here. If they are going to be very extensive then maybe we put them in the docs/usage.md instead.

Let me know if you need anything else.

Thanks!

Thank you!

[drpatelh]

Fixed in #815