new module: custom/awk_fai_to_bed

[maxulysse]

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?

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

[maxulysse]

cf https://github.com/nf-core/sarek/blob/master/modules/local/build_intervals/main.nf https://github.com/nf-core/raredisease/blob/master/modules/local/create_bed_from_fai.nf

[asp8200]

@maxulysse : Maybe I can do this one? It seems the main thing is to write some nf-test tests for the "new" module, right?

[asp8200]

@maxulysse : Concerning the proposed name of the new module - the nf-core tool doesn't like underscores in the name of modules. How about we go with custom/faitobed?

[asp8200]

Made this draft, but couldn't the nf-core module gawk be used instead?

[tdanhorn]

Since this is a stand-alone process just for awk, it looks to me like a very good use case for the gawk module. (If it were a line in some other process, a module would be overkill, but for this it seems like a perfect fit.)

[asp8200]

@maxulysse : How about I make a PR to Sarek where I replace local/buid_intervals with nf-core/gawk?

[maxulysse]

Yeah, let's see if you can make it work

[asp8200]

@maxulysse @tdanhorn @ramprasadn : What do you think about this?

[maxulysse]

@maxulysse @tdanhorn @ramprasadn : What do you think about this?

PURE GENIUS