Separate maxEE for paired-end forward and reverse reads

[naurasd]

Description of feature

Hi!

When running DADA2 as a stand-alone pipeline in R on paired-end reads, I am able to specify a vector with two different values for maxEE during the filterAndTrim step - one for forward reads, and one for reverse reads. With nf-core/ampliseq, I can only set a single integer for the --max_ee parameter, applied to both forward and reverse reads simultaneously.

I have a data set with reads from several sequencing runs. For some runs, the Illumina NextSeq data has some quality drops along the entire read length of the reverse reads only (apparently a strange but known behaviour with this platform). I am specifying different --trunclenf and --trunclenr values, but I would also like to relax --max_ee for reverse reads only.

Seeing that vectors of integers can be set for example for the --binned_quality paramater, I don't see why this wouldn't be possible for --max_ee as well?

Just a thought!

Best
Nauras

[d4straub]

Yes, absolutely correct. The parameter could be changed to accept also a list.

In the meantime, you could add a config (supply at runtime with -c) that modifies that here:

process {
    withName: DADA2_FILTNTRIM {
        ext.args = { [
            'maxN = 0, trimRight = 0, minQ = 0, rm.lowcomplex = 0, orient.fwd = NULL, matchIDs = FALSE, id.sep = "\\\\s", id.field = NULL, n = 1e+05, OMP = TRUE',
            "qualityType = \"${params.quality_type}\"",
            "truncQ = ${params.truncq}",
            "minLen = ${params.min_len}",
            params.max_len ? "maxLen = ${params.max_len}" : "maxLen = Inf",
            params.sequencing_type == "iontorrent" ? "trimLeft = 15" : "trimLeft = 0",
            params.sequencing_type in ["pacbio","iontorrent","illumina_se"] ? "maxEE = ${params.max_ee}" : "maxEE = c(${params.max_ee}, ${params.max_ee})",
            params.sequencing_type == "pacbio" ? "rm.phix = FALSE" : "rm.phix = TRUE"
        ].join(',').replaceAll('(,)*$', "") }
        publishDir = [
            path: { "${params.outdir}/dada2/args" },
            mode: params.publish_dir_mode,
            pattern: "*.args.txt"
        ]
    }
}

to something that includes "maxEE = c(2,4)" or such.

[naurasd]

Ok cool, thank you!