In the script section, is it nf-core compliant to cp/mv/rm files in the script section of a module? According to this (https://www.nextflow.io/docs/latest/working-with-files.html#copying-files), it is not but there is a dualrnaseq pipeline that I'm using that copies files using cp (https://github.com/nf-core/dualrnaseq/blob/1.0.0/main.nf).

generally not ideal and should be avoided. the dualrnaseq hasn't been updated in 4 years, maybe look at more recently maintained pipelines for patterns

I understand that the any files that are manipulated should mainly go through the input and output but is there a specific reason/s why that is not encouraged? Maybe some documentation that explains why?

Because it duplicates disk space usage in the work directories, and there's almost always no need for it.

Thank you so much!!