camelCase params duplicated with hypens

[ewels]

Bug report

Expected behavior and actual behavior

When using a param with camelCase, a duplicated copy is made with hyphens (camel-case). I've never noticed this before, but the new @nf-core schema validation now warns about these params as they are unexpected.

Expected behaviour would be to, well, not do this. 😀

Steps to reproduce the problem

params.snake_case = 'foo'
params.camelCase = 'bar'
params.multiCamelCaseParam = 'baz'

println(params)

Program output

$ nextflow run main.nf
N E X T F L O W  ~  version 21.03.0-edge
Launching `main.nf` [elegant_euler] - revision: b5f0bc6361
[snake_case:foo, camelCase:bar, camel-case:bar, multiCamelCaseParam:baz, multi-camel-case-param:baz]

More readable:

• snake_case: foo
• camelCase: bar
• camel-case: bar
• multiCamelCaseParam: baz
• multi-camel-case-param: baz

'cc @KevinMenden @Leon-Bichmann

[pditommaso]

Yes, this was a choice made in the early days, I admin, not one of the best.

[ewels]

What's more confusing is that the nextflow config command doesn't do this, only nextflow run:

nextflow.config:

params {
    snake_case = 'foo'
    camelCase = 'bar'
    multiCamelCaseParam = 'baz'
}

main.nf:

println(params)

$ nextflow config -flat .
params.snake_case = 'foo'
params.camelCase = 'bar'
params.multiCamelCaseParam = 'baz'

$ nextflow run .
N E X T F L O W  ~  version 21.03.0-edge
Launching `./main.nf` [happy_brattain] - revision: ec72fcbcb3
[snake_case:foo, camelCase:bar, camel-case:bar, multiCamelCaseParam:baz, multi-camel-case-param:baz]

This is actually a good thing in our case, as it means that we only need to add a workaround in the pipeline schema validation at run time, and don't need to patch any of the code in nf-core/tools that builds stuff with the output of nextflow config.

Phil

[pditommaso]

I think it should be fixed with a big note in the cli docs

[pditommaso]

Done ebfed09

[ewels]

Thank you!