A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

also, am I missing something or does viralrecon not do minimum depth masking of genomes?

not exposed trough params <https://github.com/nf-core/viralrecon/issues/447>

that's legit enough reason for me to put a big "DO NOT USE" over it I'm afraid

Just make a config  and patch the `-m &lt;depth-of interest&gt;`
``` 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 = { "${meta.id}.consensus" }
                publishDir = [
                    [
                        path: { "${params.outdir}/variants/${variant_caller}/consensus/ivar" },
                        mode: params.publish_dir_mode,
                        pattern: "*.{fa,txt}",
                    ],
                    [
                        path: { "${params.outdir}/variants/${variant_caller}/consensus/ivar" },
                        mode: params.publish_dir_mode,
                        pattern: "*.mpileup",
                        enabled: params.save_mpileup
                    ]
                ]
            }```

custom config is unfortunately a bit beyond the artic network users

not everyone ofc, but when we're going a recommendations for sequencing scary new virus we have to have a strong focus on usabillity

Maybe this a sign for us <@U0352U0U124> <@U04JKRB6UUR> to think about fixing this issue:
<https://github.com/nf-core/viralrecon/issues/447>
And expose the minimum depth through params

Yeah I can take a look at this and see what will need to be updated!

<@U0352U0U124> Great! You are going to take care of this issue!