Jennifer Müller

As promised the addtional log files: 1. Download of the model failed most likely due to network security issues [dragonflye_failed_to_download_model.log](https://github.com/bactopia/bactopia/files/14987638/dragonflye_failed_to_download_model.log) 2. Manual medaka model with --medaka_model flag provided [dragonflye_log_model_right_spelling_medaka_model_flag.log](https://github.com/bactopia/bactopia/files/14987636/dragonflye_log_model_right_spelling_medaka_model_flag.log) 3....

problem does not arise if I run it via _nextflow run bactopia/bactopia_ with profile docker

[Dragonflye](https://nf-co.re/modules/dragonflye) is already present as module

I tried to fix this bug and **could not recreate it on the dev or master branch**. Therefore, I want to make sure, if I understood the problem correctly: -...

To come back to the question of @asp8200, on which branch did you observe the error? I could only recreate the error on the main branch. If you pull the...

Hmm, I'm not familiar with the run time of awk. Could we run in some problems with the for-loop in your on-line awk option? Especially, with large datasets.

@SPPearce sorry for the late reply. I will not work further on this pull request. I was a bit overwhelmed by the possible options of the command and the dependencies...

Dependent on output of _vg construct_ (already in modules), _vg index_ (already in modules), and _vg pack_ [#2801](https://github.com/nf-core/modules/issues/2801)

Hello @nvnieuwk , I'm working on a pull request for the vg/call module. I'm not quite familiar with the different flag combinations for vg/call. How generic do you want to...

Yes it does. I have tested it just to be sure before I implemented the autogeneration of the samplesheet in fetchngs as csv