More diverse parameter choice for ColabFold

[Dimon821]

Description of feature

Ovchinnikov's and Steinegger's notebooks feature a broad variety of input parameters whereas the NF pipeline provides significantly less choices. I assume the parameters used are the ColabFold defaults, would it be possible to pass these parameters explicitly in the parameter JSON of the ProteinFold pipeline, such that the user can modify these easily?

The missing parameters are the number of input seeds and the number of relaxation iterations.

[tlitfin]

I think exposing lots of tool arguments as pipeline parameters might be against nf-core philosophy but you can still access them by setting the ext.args field of your config with the appropriate process label.

eg

process {
  withName: 'COLABFOLD_BATCH' {
    ext.args = '--num-seeds 1 --relax-max-iterations 2000'
  }
}