Option to trim based on Illumina 2 colour chemistry

[npatel-ah]

Hello,

Thank you for amazing work on this pipeline, it's very comprehensive.
I am wondering if there is any way to specify --2colour / --nextseq flag during trimming step. I reviewed few samples from Zymo RRBS library and sequenced with NovaSeq. All of the samples have G over call at the end of the reads, leading to high GC content. See https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/

Describe the solution you'd like

Have an option to enable or disable --2colour / --nextseq trimming capabilities, I believe --trim_nextseq in nf-core/sarek/2.7.2 does the same thing: https://nf-co.re/sarek/2.7.2/parameters#trim_nextseq

Describe alternatives you've considered

Manually trimming FastQ first and then disable "trimming" step during "nf-core/methylseq"

[sateeshperi]

@npatel-ah still interested in this feature ? wanna work with me to integrate it ?