Use local downloaded models for medaka in dragonflye module [feature]

[jenmuell]

Related To

• Bactopia
• Bactopia Tools

Is this related to a problem?
I want to test how the different polishing methods influence my dragonflye assembly and have struggle to install the medaka models for the long reads, most likely due to some network limitations. The command.log mention that I can download the model manually and afterward us the .tar.gz as input for the --model parameter, but I have issues to apply this to dragenflye since there is a restricted vocabulary, which models I can use. I have tried the --medaka_model flag of bactopia and the --dragonflye_opts "--model <>.tar.gz" option. Both lead to the same error message.

Bactopia was installed with conda and I ran it with the profile docker.

Describe the solution you'd like
Option to give dragonflye a manually downloaded medaka model with the --medaka_model flag.

Additional Information
Logs with the error messages will be added below

[jenmuell]

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
2. Manual medaka model with --medaka_model flag provided
   dragonflye_log_model_right_spelling_medaka_model_flag.log
3. Manual medaka model with --dragonflye_opts "--model" provided
   dragonflye_log_model_right_spelling_dragonflye_opts_flag.log
4. Full commands of bactopia, which lead to the error messages
   bactopia_commands.txt

[jenmuell]

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