Replace QUAST custom modules with official nf-core ones

[amizeranschi]

Description of feature

Currently there is no way to send customized parameters to QUAST via ext.args. It would be helpful to enable this feature, for example, to allow setting customized --contig-thresholds for report generation.
https://quast.sourceforge.net/docs/manual.html#sec2.3

[jfy133]

Generally you can always write your own custom config to override the default ext.args, but Indeed I don't really like giving users too much freedom.

If you have a list of the most important quast parameters that you think most people would want to modify we can add these as dedicated pipeline level parameters

[amizeranschi]

Generally you can always write your own custom config to override the default ext.args, but Indeed I don't really like giving users too much freedom.

I'm not sure what you mean here. Given how the current QUAST module looks like right now, I don't see a way that the user could pass custom arguments via ext.args, or any other variable for that matter:
https://github.com/nf-core/mag/blob/dev/modules/local/quast.nf#L19

If you have a list of the most important quast parameters that you think most people would want to modify we can add these as dedicated pipeline level parameters

I'm not familiar with all the parameters and haven't tested QUAST extensively. Right now I was looking at --min-contig, which is 500 by default, and --contig-thresholds, which allows one to customize the contig length thresholds that are used for generating the QC report.

The nf-core/mag pipeline has the --min_contig_size parameter, which selects contigs for binning and is set at 1500 bp by default. It would be useful to have a way of finding out (using QUAST) what is the number of contigs in the assembly (and the total assembled bp) at a minimum length of 1500 bp.

Two other QUAST parameters that could be useful (especially for benchmarking) are -r and --references-list.

[amizeranschi]

@jfy133 was this issue referenced by mistake in the v. 3.3.1 release PR (#764)? Because I don't think this issue was ever addressed there.

[jfy133]

Ups yes, wrong reference

[jfy133]

Note we should also replace local with offical nf-core module so ext.srgs comes as default anyway

[amizeranschi]

OK, I've now modified the title of this feature request, to better reflect how it should be solved.