Add support for more aligners

[matthdsm]

Description of feature

If and when possible, can you add support for other aligners next to bwa?

Thanks
M

[nh13]

@matthdsm can you provide a justification for other aligners, and perhaps some examples of why(IGV screenshots welcome)? I personally prefer the simplicity of one supported aligner here, versus the overwhelming options that other pipelines have. Also, this pipeline is meant to follow the fgbio best practices so I’d be also curious about needing a different aligner in case we should update the best practice.

[matthdsm]

Hi,

Thanks for the reply.
I can see the need for a robust consensus calling pipeline coming in the near future in our lab, but we are standardising all our pipelines to use snap-aligner. This has shown way better performance during alignment and downstream variant calling.

I think by using existing subworkflows for alignment this could added with relative ease. The biggest downside I see is that you won't be able to profit from the speed gains by piping data through the tools. Other than that, I should only come down to swapping out the aligner.

I can see the need to adhere to the fgbio best practices though, hence the "if and when". It's just that bwa, while still being industry standard, is starting to show its age with the advent of "next gen" aligners such as snap and dragmap.

Matthias

[nh13]

@matthdsm I think that makes a lot of sense to use different aligners. I am leery of adding a lot of conditional logic, as it gets very complicated to maintain, and opens the flood gates about supporting/implementing everybody's favorite method ("why not mine?"). I have just seen how difficult it has been for some of our clients to modify other very popular nf-core pipelines given all the logic therein.

Nonetheless, I think having a concise proposal about which method you'd like added, as well as a reasonably polished PR, would go along way to having it integrated.

[matthdsm]

Hi Nils

I'd propose adding the fastq_dna_align subworkflow. This way you minimize the logic you need to maintain (this is done on the subworkflow side) and get support for the most popular aligners. People who want something else should first add it to the relevant subworkflow.
Barring any breaking changes, this would allow a plug and play upgrade each time the subworkflow is updated.

so TL;DR: implement subworkflow, get free aligner support from upstream.

Sadly, I'm currently working on other stuff, so I won't be able to provide a decent PR in the short term. To be honest, with this issue I was hoping someone else with the same need would pick it up so it's ready when we need it 😅
Of course, if it comes down to it I'm very willing to do some work on this, time allowing.