Cleanup needed for nf-core logo / monochrome logs.

[ewels]

Started looking into warnings for #3294 and saw one about monochrome_logs being unused here:

tools/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

Line 35 in 41b4516

monochrome_logs // boolean: Do not use coloured log outputs

This seems to be a leftover from before we moved to nf-schema to print the header. The nf-core utils subworkflow no longer does this, so no longer needs the monochrome_logs option to be passed to it.

The more I started looking into it, the more I think that there is a bit of cleanup needed here.

• nf-schema has a configuration option called validation.monochromeLogs
  • We're not setting this currently, we probably should - set to params.monochrome_logs
• We have def nfCoreLogo in the nf-core subworkflow which is, as far as I'm aware, not used anywhere
• Pretty sure that the dashedLine function is only used by nfCoreLogo, so can also be deleted.
• The nextflow.config hardcodes the logo (not using the above function), with ANSI colours hardcoded. So there is no way to disable colours.

As a minimum we need to remove the unused input from the subworkflow to help solve #3294 - but we should also try to clean up this 👆🏻 so that:

• --monochrome_logs makes the nf-core logo monochrome
• There is minimal code duplication / orphaned unused code

[ewels]

Unresolved - how to fix this:

tools/nf_core/pipeline-template/nextflow.config

Lines 252 to 255 in 41b4516

	def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
	timeline {
	enabled = true
	file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"

We're not allowed def in nextflow.config any more.

We originally added it years ago to avoid filename clashes, but that's no longer needed. However, I'm not sure how to set the report directories to "${params.outdir}/pipeline_info/ without also specifying the report filename. And if I specify the report filename I don't know how to include the timestamp 🫠

So we need to either:

• Somehow specify the report directory and leave the default Nextflow filename (not possible?)
• Refactor the above code to give the entire file path, including a timestamp

[mirpedrol]

using validation.monochromeLogs will remove the colours from the logo we have hard coded in validation.beforeText. See the nf-schema code here.
But it doesn't work when setting validation.monochromeLogs = params.monochrome_logs. This looks like one of the Nextflow particularities when overriding params 🤔 do you have an idea why this could be happening? It does work 😄

[awgymer]

I don't think that monochrome_logs has been properly removed from PIPELINE_INITIALISATION where it is no longer used?

tools/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

Line 35 in 45c7879

monochrome_logs // boolean: Do not use coloured log outputs

If you make a new pipeline and check this line it should be highlighted by the LSP with Variable was declared but not used