Lauri Mesilaakso issues

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                                            Lauri Mesilaakso

feat: Add wrapper for GATK DepthOfCoverage

### Description This PR adds a wrapper for GATK DepthOfCoverage tool. ### QC For all wrappers added by this PR, I made sure that * [x] there is a test...

Add separate Nanopore input option

## Is your feature request related to a problem? Please describe At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only). ## Describe the solution you'd like...

enhancement

Add support for MGI's Atoplex kit

### Description of feature Sequencing reads from MGI's Atoplex library prep kit is not currently supported. This feature adds support for it.

enhancement