Hello, I'm using the nf-core/hic pipeline to process some public Hi-C datasets. While I was using the pipeline, I noticed that it copies output files independently of the parameter

publish_dir_mode

. For context, I normally change nf-core's default

copy

mode to

link

or

symlink

to avoid storage duplication and at the same time maintain the ability to resume. I reviewed the pipeline's code in GitHub and have noticed that

hic/conf/modules.config

has all processes hardcoded with publishDir

mode: 'copy'

in the latest stable version 2.1.0. For the

dev

version, most processes also have

mode: 'copy'

, except for

MULTIQC

. As it stands now, nf-core/hic always copies results to the output directory ignoring the parameter

publish_dir_mode

, which isn't ideal. Please let me know if I'm missing something obvious. But if I'm not, I'll be happy to change the code myself and do a Pull Request.

I don't think there is much activity in this repo at the moment, so I would suggest making the PR 😉

Ok. Thanks for the quick answer. I'll give it a go! As I am quite new to the community, I would greatly appreciate it if you could share any important rules that I should be aware of when contributing. A link to the relevant info will do marvels as well.