Add A5-miseq support

[vinisalazar]

Hi,

thank you for providing this pipeline.

Would you consider providing A5-miseq support for short-reads-only mode?

I normally use Spades (or Unicycler in this case), but I've consistently been getting better results with A5-miseq when assembling a short-reads-only dataset.

e.g. compare these two assemblies
bacass - unicycler:
Total n: 181
Total seq: 5473999 bp
Avg. seq: 30243.09 bp
Median seq: 1476.00 bp
N 50: 143598 bp
Min seq: 110 bp
Max seq: 623519 bp

a5-miseq:
Total n: 78
Total seq: 5532586 bp
Avg. seq: 70930.59 bp
Median seq: 4987.50 bp
N 50: 278625 bp
Min seq: 623 bp
Max seq: 761326 bp

It is not a huge difference, but I believe it would be a good addition to the pipeline. I'd love to make a PR myself, but I'm still not confident enough with Groovy/nextflow scripting.

Thank you for any assistance you can provide,

V

[apeltzer]

I'm going to make a maintenance release these days - feel free to work on this and try to add it to the pipeline if you want to use it :-) This is open source, so you're very welcome to do so!

[vinisalazar]

Thanks @apeltzer . At the moment I cannot dedicate time to this, but I would be interested to give it a try a couple of months from now. Will keep this issue updated if I do so.

[apeltzer]

Sounds good - whenever you find time :-)

[Daniel-VM]

Closing this issue. Please feel free to reopen it if needed.