Hi all. I just ran methylong pipeline (v2.0.0) and bumped into an issue. Would like to know your thoughts on this. The bedgraph output files it makes are empty. I ran it for 4 samples and they came out blank for every sample. I only caught it because I opened the files and checked. I ran the pileup step with

--combine-mods

( which combines 5mC and 5hmC into one call). And I think that changes how one column in the output looks. And the bedgraph step is expecting the old format, so its filter never matches anything, and it drops every row.

That sounds like a bug, could you open an issue on github? github.com/nf-core/methylong/issues

Sure!