A pipeline for prediction and annotation of obelisks

Question

[fred.s.kremer]

Hello everyone!

I have created a pipeline for the prediction and annotation of obelisks, the newly discovered class of viroid-like elements (https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1.full). Can anyone give me some feedback and maybe help in the improvement of the tool (by pull request), also in the manuscript?

https://github.com/omixlab/tormentor

[Pierre Lindenbaum]

thanks for sharing. But why system calls when you could 'just' have used a workflow manager like snakemake or nextflow ?

os.system(f'mkdir -p {spades_directory}')
step_2_return_code = run_spades(
    reads_1_trim, 
    reads_2_trim, 
    arguments.threads, 
    spades_directory, 
    stranded_type=arguments.stranded_type
)

[fred.s.kremer]

Hello Pierre!

The pipeline is still a draft, but i wanted to implement it also as a library, so users might have more control of each step ... also, i'm not very familiar with snakemake or nextflow, but i will study more about it!