Patrick Hüther

Hi @rbpisupati, thanks alot for testing this. > 1. Gives an error when few samples are single-end and others paired-end. Would be great if it can detect presence of second...

> If I remember correctly, it is trying to do paired-end mapping with filename `null` since file path isnt present in the `samplesheet.csv`. I tried to reproduce it with this...

Hi @njspix, thanks a bunch for picking this up and pushing it forward, great job! Though I have to say I'm not particularly happy with the fact that the "one-sample-one-genome"-functionality...

Don't get me wrong I'm not blaming anyone here, I think what happened is that it got decided by popular vote a while ago. So fine with me, although I...

I think this would be a nice addition, particularly for population (epi)genetics. Something similar to a design file as was done over at nf-core/chipseq by @drpatelh We need to think...

There is now a [dsl2 branch](https://github.com/nf-core/methylseq/tree/dsl2) with this functionality. Please give it a try :+1:

Hi @ewels, Thanks for picking this up again, I hadn't looked at this for a (quite a) while. Just as a heads up, there are few caveats regarding the removal...

> sorry it's taken me so long to get around to helping you with it. No worries, great that you brought it up again so we can have this discussion...

> @phue : how did you manage to configure Pages that way ? For instance, here at the Sanger institute, we use gitlab.internal.sanger.ac.uk and pages.internal.sanger.ac.uk, so it still wouldn't work....

The sole purpose of that `-w` flag was to enable bind-mounting of the nextflow work directory when using public container images. Now that `charliecloud` soon supports `overlayfs`, it should be...