SV karyogram for non-human species in SV report

[phpeters]

Is your feature related to a problem?

When using non-human species with a different number/description/size of chromosomes, the SVs don't get nicely plotted in the SV report.

The argument --genome in the def karyoplot in bin/workflow_glue/report_sv.py is not really changeable by hand.
Furthermore, available options are only hg19 and hg38 from package ezcharts (in folder /opt/custflow/epi2meuser/conda/lib/python3.10/site-packages/ezcharts/data/reference in the apptainer container ontresearch/wf-common-shaabceef445fb63214073cbf5836fdd33c04be4ac7).

Describe the solution you'd like

A parameter for the nextflow pipeline (--ownChromSizes or so) to provide one's own file with chromosome names and sizes. This would mean to adapt

args.genome in bin/workflow_glue/report_sv.py and
the process report in modules/local/wf-human-sv.nf

Describe alternatives you've considered

At the moment I re-run workflow-glue report_sv by hand after the pipeline finishes and use a relative path to escape the ezcharts-path and to get to my own chromosome-size file (see example command below and example plot for Arabidopsis)

$ ls /tmp
tair/
tair.chrom.sizes.gz

$ apptainer exec  work/singularity/ontresearch-wf-common-shaabceef445fb63214073cbf5836fdd33c04be4ac7.img \
        wf-human-variation/bin/workflow-glue report_sv \
        mysample.wf-human-sv-report.html  
        --vcf my_sample.wf_sv.vcf.gz \
        --params params.json \
        --params-hidden 'help,schema_ignore_params,show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,min_read_support,min_read_support_limit,fastq_only' \
        --versions versions.txt \
        --revision null \
        --commit null \
        --output_json "my_sample.svs.json" \
        --workflow_version 2.6.0 \\
        --genome "../../../../../../../../../../../../tmp/tair"

Additional context

Thanks for the work you are putting in!
All the best!
Philipp