James A. Fellows Yates
James A. Fellows Yates
Basically what Jim said, but we can probably improve that to add `-depth 3` or something to restrict how deep it goes into...
Speaking with @prototaxites we discussed a bit more about this. My general concern was whether we would loose columns that are in QUAST but not SEQKIT, which there is a...
> Curious -is anyone is currently working on this? I would be interested in this feature and potentially open to working on it if no one else is. Nope, I...
I think this should be more of an enchancement as it's more of an edge case that is pushing the internal tools to the limit, rather than the pipeline itself....
Conceptually I think that makes reasonable sense to me! We are already now getting the length stats of each bin (`binning.nf`) no reason to not push that back?
Yes exactly that's what I meant by 'pushing back'! Maybe you can add this to your list @d4straub ? 😬
I'm very very sorry @dbajpp0 this completely slipped out of my TODO list Unfortunately this appears to be an error with VCF2Genome. I would suggest going into the working directory...
Compress FASTA files with contigs and scaffolds using bgzip instead of gzip, to enable file indexing
Do you have examples of what tools require this type of gzipping? This will require quite a fundamental change of the official nf-core modules, so I want to check if...
Compress FASTA files with contigs and scaffolds using bgzip instead of gzip, to enable file indexing
> I've been looking into QC tools for finding misassemblies from reads mapped to contigs. Two promising examples are DeepMAsED (Deep learning for Metagenome Assembly Error Detection) and ResMiCo (Residual...
Theoretically no reason not to, but it would break the website rendering currently I imagine. What would the benefits be though? I don't see an issue between configs/modules having different...