Enable genome specification (mgatk)

[agiguelay]

Hello,

Thank you for the great work! 🥇
I'm running the pipeline on mouse data and got the following error concerning mgatk:

User specified mitochondrial genome does NOT match .bam file; correctly specify reference genome or .fasta file

I could solve it by modifying the rules/mgatk.smk:

    mgatk tenx -i {params.bam} -n {wildcards.sample} -o {OUTDIR}/{wildcards.sample}/mgatk/ \
    -bt CB -b {OUTDIR}/{wildcards.sample}/cellranger_count/outs/filtered_peak_bc_matrix/barcodes.tsv \
--mito-genome mm10 
    """

Could it be possible to add this as a parameter for the future versions ?

Thanks again :)