I am one of the developers of the nf-core/riboseq pipeline that we have started work on recently. It is now recognised as 'in-development" by the nf-core community but we still have a lot of work to do. I am trying to develop a RiboCode module so that the pipeline can support ORF calling as an option.
Firstly, I wanted to let you know about this effort and secondly, I have a few suggestions regarding the usability of the tool.
GTF parsing - this could be made to work on a wider range of GTF variants. Much of this can be handled by the GTFupdate subtool. eg GTFupdate should sort the gtf file
Switch to pyfaidx - Brent Pedersen the developer of pyfasta archived it back in 2018. This should not be too arduous but unfortunately it is not a straight swap.
I am happy to help with these and will likely make PRs here for them as I need them
Hi Developers!
I am one of the developers of the nf-core/riboseq pipeline that we have started work on recently. It is now recognised as 'in-development" by the nf-core community but we still have a lot of work to do. I am trying to develop a RiboCode module so that the pipeline can support ORF calling as an option.
Firstly, I wanted to let you know about this effort and secondly, I have a few suggestions regarding the usability of the tool.
GTFupdatesubtool. egGTFupdateshould sort the gtf fileI am happy to help with these and will likely make PRs here for them as I need them