Improvements in forked repository: KmerFinder, Estimation of Reference Genome, Custom Quast, and Custom MultiQC Reports about bacass

[d4straub]

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 is good practice.

I browsed over it and there were some minor points, e.g. a param with skip_* (such as skip_kmerfinder) shouldnt be by default true I think. I am not very much into MultiQC, so I am not sure why a custom module is needed, I thought MultiQC can be configured to do almost anything, but you have your reasons I assume.

So yes, I think that would be nice to add into the nf-core repo.

[Daniel-VM]

Apologies for the late response.

Great, I still have to fix some minor points in the code and run additional tests. Once it's ready, I will let you know.

Regarding the MultiQC custom table at the beginning of the report, it will play a similar role to the default "General Stats" table. However, in the custom table you can add metrics from both supported and non-suported MultiQC tools (in fact, any data you wish to). This custom table contains most of the key metrics that my group needs to check in bacterial genome assembly analysis. Since not all the tools we check have a supported module in MultiQC, we gather all the metrics from these tools (that we use for analysis) and consolidate them in a single table. The pipeline also exports this table in CSV format.

[d4straub]

Looking forward!

I see, such an overview table is certainly a good idea.