I'm new to HiC, here is my newcomer questions / suggestions about https://nf-co.re/hic/2.1.0/parameters/: for the

--restriction_fragments

flag the help text says: "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the —restriction_site option". It seems to me that setting

--digestion

also sets the

—restriction_site

option, and hence the help text could say: "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --digestion or —restriction_site option"? Also, do I understand correctly that

--restriction_site

and

--ligation_site

are set automatically if you set

--digestion

? If yes, then a short help text there would also be nice. I'm happy to do a PR :)

Feel free to put in a PR! The beauty of the community here is that everyone is welcome to contribute, no permission required 😀

Make sure you build off the dev branch, as the 2.1.0 release looks like it was 3 years ago