nextflow config doesn't parse main.nf

[ewels]

When running nextflow config, things defined in main.nf are not picked up. For example:

main.nf:

params.one = 'this is defined'

nextflow.config:

params.two = 'this is also defined'

$ nextflow config .

params {
   two = 'this is also defined'
}

This can be a little confusing sometimes, if the config is split between the two.

Phil

[drpatelh]

This came up again yesterday because nf-core lint is set to only parse nextflow.config for the standard parameters we require to be defined in the template.

e.g. I have actually defined the standard parameter in main.nf because it's mandatory and doesn't necessarily need to be initialised in nextflow.config. However, the linting still generates a warning.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[ewels]

@pditommaso - is this issue affected by #889?

[pditommaso]

Unfortunately no.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.