Input in first process missing

[luisas]

The bed process does not have any input specified but still accesses to file specified by the params.

This I think is dangerous, normally files used in the script are passed as input. I already got nf pipelines failing because of this and i modified it as I need in my forked version but maybe you want to have a look on it :)

[tdelhomme]

@luisas Thanks for this remark! If you want to make a PR on this, that would be ok for us !