Simon Pearce
Simon Pearce
Hi @jenmuell , do you need some help to finish this?
Yeah, I know that dealing with pairs is a pain, particularly when you start thinking about cross chromosomes or supplementary/secondary alignments.
> - For duplex-sequencing, the UMIs help identify the original source strand of the molecule, so dummy values would would cause all reads to be on the top-strand. Hmm, I...
I think that the best way to actually do this is to up the allowable edit distance to something larger than the umi_length, which will make all the UMIs to...
This has already been done [upstream in modules])https://github.com/nf-core/modules/blob/master/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf), and then propagated into sarek.
Can you please add some tests via `nf-core modules test msisensorpro/msitumoronly`
Looks generally good, few minor points. Is the meta.yml not updated? Presumably that still points at the old broad institute github link.
Hey @adamrtalbot , shall we get this finished off and merged in?
I have a half-done conversion to nf-test actually
Superceded by #6079 as I couldn't edit Adam's branch.