GenomicsDBImport : Mismatching intervals for input-vcf-files and bed-interval-file

[asp8200]

Description of the bug

There seems to be a mismatch in the GenomicsDBImport process between the intervals for the input-vcf-files and the input-interval-bed-file. Here is an example:

gatk --java-options "-Xmx6553M" GenomicsDBImport \
    --variant HG002.haplotypecaller.chr16_46380683-90228345.g.vcf.gz --variant HG003.haplotypecaller.chr2_89753993-90402511.g.vcf.gz \
    --genomicsdb-workspace-path chr16_46380683-90228345.joint \
    --intervals chr16_46380683-90228345.bed \
    --tmp-dir . \
    --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader 

More info on Slack:

https://nfcore.slack.com/archives/CGFUX04HZ/p1686902281599399?thread_ts=1686493658.456969&cid=CGFUX04HZ

Command used and terminal output

nextflow run main.nf -profile docker --input /home/ubuntu/test_data/mapped_joint_bam_HG002_HG003_1perc_of_40x.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --skip_tools haplotypecaller_filter

### Relevant files

_No response_

### System information

_No response_