nf-core
Hard-coded settings for Bismark
I noticed two hard-coded settings for bismark that are only for paired-end calls
https://github.com/nf-core/methylseq/blob/62d30e1d06d194047a372be60e4755fd8d0e9281/main.nf#L511-L512
Should these be moved into parameters?
Hi @cjfields,
We certainly could - however, because the pipeline runs trimming with Trim Galore prior to alignment, I haven't felt the need to before. The number of bases to trim is configurable. Is there a context where it would make sense to alter both, or one and not the other?
Phil
We've had instances where we would like to rerun the workflow but tweak the bismark methylation extraction step w/o having to rerun the full pipeline.
In particular I noticed a technology-specific methylation bias from RRBS data at the 5' end of the sequence (a single base) and wanted to remove it to prevent false-positive calls; this is for UMI-based deduplication. The data are single-end reads (and so I needed to introduce the parameters for this purpose), but I happened to notice the hard-coded options in the paired-end step.
We're currently doing this on a fork, with the UMI code in a branch:
https://github.com/HPCBio/methylseq/blob/0a1aafac534449bd2591a15752b0f1631c7e6c2a/main.nf#L644
We've had instances where we would like to rerun the workflow but tweak the bismark methylation extraction step w/o having to rerun the full pipeline.
Yup. that's a good reason! Can certainly add it, very easy to do.
Separately, NuGEN UMI support would be nice to add. It's quite a common kit type, there's a good chance that we'll also want to run with this in the future too. Would be great if we can merge that into the main release some time :)
Separately, NuGEN UMI support would be nice to add. It's quite a common kit type, there's a good chance that we'll also want to run with this in the future too. Would be great if we can merge that into the main release some time :)
That's the long-term goal, as well as adding UIUC support for running this on our various cluster resources :)
Sounds great!
Would be good to add you guys to the list of contributors too in that case 😉 http://nf-co.re/about - just make a PR adding yourself to https://github.com/nf-core/nf-co.re/blob/master/nf-core-contributors.yaml along with a colour and white logo in SVG (I can help with these if you want).
Just had a look and it seems that these options are now set via parameters:
https://github.com/nf-core/methylseq/blob/44b80aa2bf6e8f11e23d506227bbd7293c108cb1/conf/modules.config#L214-L215
They're still set to 2 by default in nextflow.config:
https://github.com/nf-core/methylseq/blob/44b80aa2bf6e8f11e23d506227bbd7293c108cb1/nextflow.config#L66-L67
..but they're params and in the schema so should now be very easy to adjust and customise.
So I think that this issue can be closed as completed ✨