Monochrome logs is option in functions rather than global parameter

[adamrtalbot]

This changes monochrome logs to being an option in paramsSummaryLog(), paramsSummaryMap() and paramsHelp().

This makes the structure more flexible for pipeline developers who can now use params.monochrome_logs or handle it with their own tooling.

Fixes #99

[adamrtalbot]

@nvnieuwk a possible option here would be to default it to params.monochrome_logs, false if params.monochrome_logs does not exist? Equivalent to:

def monochrome =  params.monochrome_logs != null ? false : params.monochrome_logs

This would make it backwards compatible, but also make it complicated for developers (unexpected behaviour).

[nvnieuwk]

I'm all for backwards compatibility! Thanks for the contribution

[nvnieuwk]

I like this but my main concern is now that we have two positional arguments to the function. This means you have to specify the schema if you want to specify the monochrome_logs argument too.

You can have a look at the .fromSamplesheet() factory for an example on how to handle this:

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Line 150 in 7ca22a4

public DataflowWriteChannel fromSamplesheet(

(which uses the same method as core nextflow functions with optional arguments)

[adamrtalbot]

I like this but my main concern is now that we have two positional arguments to the function. This means you have to specify the schema if you want to specify the monochrome_logs argument too.

You can have a look at the .fromSamplesheet() factory for an example on how to handle this:

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Line 150 in 7ca22a4

public DataflowWriteChannel fromSamplesheet(

(which uses the same method as core nextflow functions with optional arguments)

Thanks, not sure I understand which bit I'm supposed to be looking at though? Should I add the arguments as the Map options?

[nvnieuwk]

Yes and some code that looks if the option is supplied like here:

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Lines 158 to 159 in 7ca22a4

	def String schemaFilename = options?.containsKey('parameters_schema') ? options.parameters_schema as String : 'nextflow_schema.json'
	def Boolean skipDuplicateCheck = options?.containsKey('skip_duplicate_check') ? options.skip_duplicate_check as Boolean : params.validationSkipDuplicateCheck ? params.validationSkipDuplicateCheck as Boolean : false

[adamrtalbot]

I've done it now but I'm not sure it's reading from the optional args correctly, can you check for me?

[edit] hold on, git faff...

[adamrtalbot]

OK I've pushed the changes but it doesn't work because of positional args stuff. Don't really have any more time to look at it I'm afraid.

[adamrtalbot]

Oh! I seem to have fixed it. Need to update docs.

[nvnieuwk]

Thank you I will look at it in detail when I got some more time, it does look very good at first glance though!

[mirpedrol]

LGTM, thank you!
My only comment is that if this is now a parameter from the plugin, we should refactor to monochromeLogs to follow the Nextflow convention.

edit: could we refactor the argument name in the options map, but allow both parameters params.monochrome_logs and params.monochromeLogs when retrieving the global parameter? The nf-core template is using params.monochrome_logs in other functions, such as creating the logo or formating emails. But other non-nf-core pipelines will use params.monochromeLogs as nextflow params are in camelCase

[adamrtalbot]

I agree. So

LGTM, thank you! My only comment is that if this is now a parameter from the plugin, we should refactor to monochromeLogs to follow the Nextflow convention.

edit: could we refactor the argument name in the options map, but allow both parameters params.monochrome_logs and params.monochromeLogs when retrieving the global parameter? The nf-core template is using params.monochrome_logs in other functions, such as creating the logo or formating emails. But other non-nf-core pipelines will use params.monochromeLogs as nextflow params are in camelCase

Do you want it in this PR or a separate one?

[mirpedrol]

Do you want it in this PR or a separate one?

Can be added to this PR :) Should be a small enough change

[adamrtalbot]

If someone sets monochrome_logs and monochromeLogs differently, which one should take precedence?

[adamrtalbot]

Current priority:

1. Function argument
2. params.monochrome_logs
3. params.monochromeLogs

def Boolean useMonochromeLogs = options?.containsKey('monochrome_logs') ? options.monochrome_logs as Boolean : 
    params.monochrome_logs ? params.monochrome_logs as Boolean :     
    params.monochromeLogs  ? params.monochromeLogs as Boolean :
    false

[mirpedrol]

sounds good!

[nvnieuwk]

LGTM, thanks @adamrtalbot

[adamrtalbot]

I don't have permission to merge but this is good to go from my end 👍

[adamrtalbot]

Oh, unless you want me to extend the tests. I haven't looked too deeply into that yet.

[nvnieuwk]

Oh yes more tests won't hurt anybody 💯