would it be possible to add an additional argument for

loci_binsize

to the ASCAT module? This would allow the module to be used with long-read data (as detailed in ASCAT docs here). I would be happy to do this myself if there is interest.

Ugh, ASCAT is so far from our current module pattern. We should be setting static parameters like that just using

ext.args

, but ASCAT predates that as far as I know. And nobody wants to take responsibility to overhaul this module... Yes, I think you can just add yet another argument and we continue to ignore the non-conformity

yes i was surprised when i saw it. but sounds good, i’ll plan on working on this in the upcoming weeks

download.jpeg

I feel like we could remove a bunch of the arguments that are only being used in the

prepareHTS

command

@Susanne Jodoin did a lot of work as well. iirc using

ext.args

as string (as usual) was tricky because they were not used in a single place. In general, this should probably be converted into a proper script with arguments

Hi, I haven't worked on ascat in a long time, but it would make sense to improve and update this and comply with current standards

all sounds good! admittedly I haven't contributed to nf-core/modules before. Do I just follow the instructions here for this?

Yes! (Except skip anything about creating a new module). IN principle, fork the repo create a branch, update what needs updating, make sure the tests pass, open a PR to the nf-core/repo, pray the tests pass their as well and get some reviews

awesome, thanks @Rike Hanssen! 🙂