new module: vg/call

[nvnieuwk]

Is there an existing module for this?

• [X] I have searched for the existing module

Is there an open PR for this?

• [X] I have searched for existing PRs

Is there an open issue for this?

• [X] I have searched for existing issues

Are you going to work on this?

• [ ] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

[lrauschning]

Hm, had a brief look at this just now – I think for this to be neatly incorporated into nf-core, we would first need modules for vg augment, vg map and maybe vg autoindex incl. appropriate tests (as the output of some of these steps may not be deterministic). I'll see if I manage to get (some) of that done at the hackathon, but that is a lot of work for adding one module.

[nvnieuwk]

Awesome thank you! Can you create issues for all these new modules and add them to the project board? Maybe you'll get some help with them that way

[jenmuell]

Dependent on output of vg construct (already in modules), vg index (already in modules), and vg pack #2801

[jenmuell]

Hello @nvnieuwk ,

I'm working on a pull request for the vg/call module. I'm not quite familiar with the different flag combinations for vg/call. How generic do you want to include all flag combinations of vg/call (-k, -k -v, -k -r, -k -v -r)? There are also some dependencies with vg/construct like the -I flag for the fasta file present.

Maybe you can support me with some this?

[nvnieuwk]

Hi, please read the guidelines for this (https://nf-co.re/docs/contributing/modules#new-module-guidelines-and-pr-review-checklist) You'll find all answers there, but don't be afraid to ask me if something's not clear