Daniel Straub
Daniel Straub
Hm thats a rather emotional plea for a simple method. I do think that the [decontam documentation](https://benjjneb.github.io/decontam/vignettes/decontam_intro.html) is not too ambiguous. Decontam implements a method that is using control samples,...
Duplicate of https://github.com/nf-core/ampliseq/issues/608? If yes please close.
In that case I propose a demultiplexing subworkflow that contains cutadapt & seqkit to bundle the tools. I agree that it would be good to track stats for demuptiplexing, probably...
Looks actually very interesting to me. But I do not have experience with those tools and did not run the branch. I trust your judgment for now that this indeed...
Looking forward! I see, such an overview table is certainly a good idea.
I am not sure whether that is still an issue. Because the pipeline is supposed to be for assembly, I think its fine when the pipeline fails when no contig...
I do not run mag in offline mode, but that should work nowadays
That question would be better asked via nf-core slack (see https://nf-co.re/join) channel "mag". But because I am already here, short answers: 1. once per row, i.e. once per illumina sample...
With time the pipeline grows and the pipeline bases on assembly. I think all tools that are not based on assembly should be rather realized in other pipelines. Otherwise the...
As far as I know there are no new thoughts except that the pipeline is getting huge, additions should be kept at a minimum. I still think that nanopore-only assembly...