Daniel Straub

I close this in favor of https://github.com/nf-core/mag/issues/383

I close this in favor of https://github.com/nf-core/mag/issues/409

Hi, that sounds good. Yes, a PR would be great! Probably `params.busco_clean` to have the tool name at the start (this isnt a standard, but I more and more think...

> is there anywhere outside of nextflow_schema.jsonand nextflow.config that the parameter needs to be documented? CHANGELOG, activate in one of the test profiles that the setting will be tested

There is a nf-core module for bakta in https://nf-co.re/modules/bakta, so adding it to the pipeline should be relatively easy with [nf-core tools](https://nf-co.re/tools/) using command `nf-core modules install bakta` following https://nf-co.re/tools/#install-modules-in-a-pipeline

Hm, I do not use `-params-file` routinely, but I did think it does not need those curly brackets? I thought it looks like described in https://nf-co.re/ampliseq/2.4.0/usage#setting-parameters-in-a-file? Could you test whether...

I had success at least until SKEWER was finished with ``` nextflow run nf-core/bacass -r 2.0.0 -profile test,singularity nextflow run nf-core/bacass -r 2.0.0 -profile test,docker ``` using `N E X...

It would be great to have flye in here, but I do want to highlight that currently a template update would be really necessary.

I actually made very good experience for nanopore assembly with dragonflye (in nf-core modules: https://nf-co.re/modules/dragonflye), the results were close to identical with trycycler results, but execution of the former was...

Trycycler will require large effort to automatize. For example https://github.com/rrwick/Trycycler/issues/47 So Dragonflye is the way to go for now I think.