Custom configuration of modules

Within viralgenie, all modules (tools, eg. FASTP, FASTQC) can be ran with specific arguments. The pipeline has a default configuration but this can be overwritten by supplying a custom configuration file. This file can be provided to viralgenie using the -c Nextflow option.

To see which specific arguments or variables are used for a module or tool, have a look at the modules.config file. Here the arguments of a module is specified as followed:

withName: IVAR_CONSENSUS {
    ext.args = [
        '-t 0.75',          // frequency to call consensus: 0.75 just the majority rule
        '-q 20',            // minimum quality score of base
        '-m 10',            // minimum depth to call consensus
        '-n N'              // Character to print in regions with less coverage
    ].join(' ').trim()
    ext.args2 = [
        '--count-orphans',  // Do not skip anomalous read pairs in variant calling.
        '--max-depth 0',    // Maximum number of reads to start to consider at each location, 0 means no limit
        '--min-BQ 20',      // Minimum base quality
        '--no-BAQ',         // Disable probabilistic realignment for the computation of base alignment quality
        '-aa',              // Output absolutely all positions, including unused reference sequences
    ].join(' ').trim()
    ...
}

In this example, the IVAR_CONSENSUS module is configured with the arguments -q 20 -m 10 for the tool ivar consensus and --ignore-overlaps --count-orphans --max-depth 0 --no-BAQ --min-BQ 0 for samtools mpileup as iVar uses the output of samtools mpileup directly.

Tip

The ext.args and ext.args2 are used to specify the arguments for the tool. If unsure which tools uses which arguments (ivar:ext.argsand samtools:ext.args2), have a look at the nextflow module file directly! For example, at modules/nf-core/ivar/consensus.nf, "\(args" and "\)args2" are used to specify the arguments for the tools:

"""
samtools \\
    mpileup \\
    --reference $fasta \\
    $args2 \\               # can be modified with ext.args2
    $bam \\
    $mpileup \\
    | ivar \\
        consensus \\
        $args \\            # can be modified with ext.args
        -p $prefix
...
"""

In case we do want to modify the arguments of a module, we can do so by providing a custom configuration file, the easiest way to do this would to then just copy a segment from the modules.config and modify the arguments. This way, none of the other configuration will get lost or modified. For example, setting the minimum depth to call consensus to 5 and the minimum quality score of base to 30 for the IVAR_CONSENSUS module:

custom.config

process {
    withName: IVAR_CONSENSUS {
        ext.args = [
            '-t 0.75',
            '-q 30',            // changed
            '-m 5',             // changed
            '-n N'
        ].join(' ').trim()
        ext.args2 = [
            '--count-orphans',
            '--max-depth 0',
            '--min-BQ 30',      // changed
            '--no-BAQ',
            '-aa',
        ].join(' ').trim()
        ...
    }
}

Warning

Make sure you include the process{} section.

Next, supply the file to viralgenie using the -c Nextflow option:

nextflow run Joon-Klaps/viralgenie \
    -profile docker \
    -c custom.config \
    --input samplesheet.csv ...

Tip

This guide not entirely clear? Also have a look at the nf-core guide for customising tool arguments.