Conceptual error in process selector documentation

[saulpierotti]

Hi, the documentation for this seems inaccurate to me. While the first part is true that the withName selector applies also to the original name of a module, not only the import name, in my usage experience it does also apply to the import name. For example if I have a process named FOO and I import it with import FOO as BAR, a withName:BAR selector will work, and also a withName:FOO selector will. The documentation suggests that only withName:FOO works, which I believe to be incorrect.

[netlify]

✅ Deploy Preview for nextflow-docs-staging ready!

Name	Link
🔨 Latest commit	41c3cc4
🔍 Latest deploy log	https://app.netlify.com/sites/nextflow-docs-staging/deploys/659f6ebac7d9240008f0f647
😎 Deploy Preview	https://deploy-preview-4416--nextflow-docs-staging.netlify.app/config
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

---

To edit notification comments on pull requests, go to your Netlify site configuration.

[bentsherman]

If this is the case then we should probably change Nextflow to not apply process selectors for the base name to aliases.

[saulpierotti]

I actually find it useful to have it this way - I can have the same module and import it with two different aliases, and then have it run with different parameters/modes according to the alias. An example is https://nf-co.re/modules/stitch, which I import once for generating the input only with certain ext.args, and once for actually running the imputation with other ext.args.

Or for example a very general module like the plink2 module. I may want to use it several times for doing different things and manage it via different ext.args.

[mribeirodantas]

It seems to be the case, I can reproduce on my side, @bentsherman.

.
├── main.nf
├── modules
│   └── foo
│       └── main.nf
└── nextflow.config

3 directories, 3 files

./main.nf

include { FOO        } from './modules/foo/main.nf'
include { FOO as BAR } from './modules/foo/main.nf'

workflow {
  FOO()
  BAR()
}

nextflow.config

process {
  withName: FOO {
    cpus = 1
  }
  withName: BAR {
    cpus = 2
  }
}

./modules/foo/main.nf

process FOO {
  debug true

  output:
  stdout

  script:
  """
  echo ${task.cpus}
  """
}

Output:

N E X T F L O W  ~  version 23.10.0
Launching `main.nf` [trusting_colden] DSL2 - revision: 466eb880a9
executor >  local (2)
[9f/cf382e] process > FOO [100%] 1 of 1 ✔
[0e/748233] process > BAR [100%] 1 of 1 ✔
1

2

[bentsherman]

Fair enough, I guess if you don't want the base config to be propagated to aliases then you can simply not use it and alias every process inclusion.

[bentsherman]

cc @marcodelapierre

consider folding this PR into the module config #4510

[bentsherman]

Closing in favor of #4510