So, mainly focus on the missing subworkflow, which is the annotation part, rather than start the updates from start to end. Could do that. I made a list of the modules that we will need to nf-core, based on Eleftherios' suggestions:

jellyfish (C++), bioconda: <https://bioconda.github.io/recipes/kmer-jellyfish/README.html#package-package%20&#x27;kmer-jellyfish&#x27>; 
transrate (Ruby), bioconda:
<https://bioconda.github.io/recipes/transrate/README.html#package-package%20&#x27;transrate&#x27>; 
rnaquast (python), bioconda:
<https://bioconda.github.io/recipes/rnaquast/README.html#package-package%20&#x27;rnaquast&#x27>; 
trnascan-se (C/perl): bioconda:
<https://bioconda.github.io/recipes/trnascan-se/README.html#package-package%20&#x27;trnascan-se&#x27>; 
trinotate (perl/JS): bioconda:
<https://bioconda.github.io/recipes/trinotate/README.html#package-package%20&#x27;trinotate&#x27>;