Allow the user to specify additional fgbio options

[lbeltrame]

Description of feature

Many modules support this, but it's not hooked in the pipeline as far as I can tell.
This is important to pass some options in IDT UMI based kits as detailed in https://sfvideo.blob.core.windows.net/sitefinity/docs/default-source/user-guide-manual/analysis-guideline-xgen-udi-umi-adapters-processing-sequence-data-with-unique-molecular-identifiers-(umis).pdf?sfvrsn=d0aa3207_40

[SPPearce]

All the modules should have the ability to take an external args via a config, even if not exposed as a parameter in the pipeline.

[lbeltrame]

I saw a variable called ext.args.fgbio, but I think it's applied to all fgbio modules?

If that's the case, perhaps an example (in the future) might be a good addition to the docs. (I already run custom configurations but I'm never sure I did things correctly).

[SPPearce]

https://nf-co.re/docs/usage/getting_started/configuration#customising-tool-arguments might help.
For instance the pipeline contains FGBIO_FILTERCONSENSUSREADS as a local module.
The code for this module has (focussing on the relevant bits):

    def fgbio_args = task.ext.fgbio_args ?: ''

    fgbio \\
        ...
        FilterConsensusReads \\
        ...
        $fgbio_args \\

which means that if task.ext.fgbio_args is defined, it will pass whatever is given into the fgbio FilterConsensusReads command when it executes.

So if you provide an additional config file with:

process {
    withName: FGBIO_FILTERCONSENSUSREADS {
        ext.fgbio_args= "--reverse-per-base-tags"
  }
}

Then this additional --reverse-per-base-tags will be passed to the fgbio tool.
Note in general nf-core modules it would usually be task.ext.args and task.ext.args2 etc, but in the local module they are fgbio_args and samtools_args for instance here.

[lbeltrame]

All right, I'll see about this then. Probably this needs to be closed.

[SPPearce]

If there are specific options that would be needed for specific kits, they could be added as a parameter.
A parameter is much more user friendly than requiring a config file