@Jonathan Manning started to update hisat2/build for strict syntax, so I replace the params for memory by an input, but that led me to a tiny trip #C073GFZ68PR, and here is what I now propose for hisat2 https://github.com/nf-core/modules/pull/12838 Basically: • updating everything (hisat2 and samtools) • moving away the meta strandness from the modules, we should really be doing that via args anyway • strict syntax Let me know if you see things that you think shouldn't be done. It is definitively not my #C0749PAEU9F

At ECCB, you guys can sort it out 🙂

Made a PR for you: https://github.com/nf-core/rnaseq/pull/1913