Daniel Straub

icon indicating a website link https://www.info.qbic.uni-tuebingen.de/

icon company Quantitative Biology Center (QBiC) icon location Tübingen, Germany icon location Bioinformatics Research Scientist at the Quantitative Biology Center (QBiC) in the realm of Computational Microbiology

Results 189 comments of Daniel Straub

Check GTDB database integrity before proceeding with GTDB-Tk classify workflow

Thanks for bringing this up! Sounds like a good idea.

Help running in offline cluster

@HadrienG any progress here?

Including functional profile step

I absolutely agree! I did not find time however to add HUMAnN3 to nf-core/tools, my [attempt](https://github.com/nf-core/modules/pull/1089) failed because lack of time. I do think that this should be implemented.

Set minimal contig length for metaBAT2 to 1,500 if the provided value is smaller

Yes, agreed, that should be done.

Add Bakta as alternative to Prokka

Not sure if its actually a good idea to replace Prokka, because: > Prokka is a software tool to annotate bacterial, archaeal and viral genomes whereas Bakta is only for...

Sharing an issue when I use nf-core/mag pipeline

Thanks for formatting it. Unfortunately that is not a very informative error message. @bbagy Could you try: - resume the pipeline, maybe it was a temporal system hickup (start the...

Sharing an issue when I use nf-core/mag pipeline

> I am not sure it is helpful information, but the pipeline was ok when I use raw fastqs. I got this error, when I use fastqs that was filtered...

Sharing an issue when I use nf-core/mag pipeline

Well, it is very well possible that with too less reads there is no proper genome bin formed because of too less data. Could you have a look in `results/GenomeBinning/bin_summary.tsv`?...

BUSCO creates a huge number of files - add a flag to remove some of these?

If I understand you right than you are talking about the entire file system, i.e. including the `work` folder from nextflow, not just the `results` folder. If yes, then I...

BUSCO creates a huge number of files - add a flag to remove some of these?

Oh wow, file limits on the scratch partition, never heard of that! Do you have an idea what directories of the process hold many files? Haven't gotten any example at...