After checking your source code, I think that in order to add a new tool or step, I should first add the module in modules/nf-core/<tool> with a test folder, .yml files and the .nf file, then edit the corressponding step's subworkflow (e.g. assemble) and add the option to take this tool. Are there any files that must be changed? NextDenovo takes two files: input.fofn which contains one read file per line, and config.cfg file which takes a number of options like the mode and the type of reads. For my data, nextdenovo performed very well and it was way faster than flye and had better N50 and #contig. I will test hifisam --ont since I wil need to compare a lot of tools. Thank you very much for your help!