[DOC] Document full parameters of iVar consensus

[corneliusroemer]

I've tried to figure out how exactly you call iVar consensus by default, to understand some issues with artifactual reversions and frameshifts.

However, I could figure out the complete default command that is run.

You have documented one option here: https://nf-co.re/viralrecon/2.5/parameters#min_mapped_reads but I can't see how it flows through the code.

In the module, you allow passing extra args, but I can't find out what they are.

Are they set to anything at all by default? If so what are default args?

The args end up here: https://github.com/nf-core/viralrecon/blob/master/modules/nf-core/modules/ivar/consensus/main.nf#L25

[saramonzon]

Hi @corneliusroemer !

All default parameters are in conf/modules_illumina.config for all processes.

For ivar consensus default parameters are:

viralrecon/conf/modules_illumina.config

Lines 556 to 562 in 3ee1fe9

	if (!params.skip_consensus && params.consensus_caller == 'ivar') {
	process {
	withName: 'IVAR_CONSENSUS' {
	ext.args = '-t 0.75 -q 20 -m 10 -n N'
	ext.args2 = '--count-orphans --no-BAQ --max-depth 0 --min-BQ 0 -aa'
	ext.prefix = { "${meta.id}.consensus" }
	publishDir = [

You can change them using a custom.config file and pass it to nextflow using -c as follows changing the desired ivar params:

process { 
         withName: 'IVAR_CONSENSUS' { 
             ext.args = '-t 0.75 -q 20 -m 10 -n N' 
        }
}

I hope this was what you were asking :)

[drpatelh]

Will consider this as answered but we should probably add some more comprehensive docs for this sort of thing to the website. Realised I added docs for updating custom resource requests and containers to the pipeline template but not for tool-specific ext.args.
https://nf-co.re/viralrecon/2.5/usage#custom-configuration

Created a separate issue here:
nf-core/website#1643

Ping @jfy133