Run pipeline with vg deconstruct parameters CI action takes too long

### Description of feature

Run pipeline with vg deconstruct parameters (--vcf_spec "gi|568815561:5,gi|568815567:25")
**5h 27m 8s** (still running)

https://github.com/nf-core/pangenome/actions/runs/14759524108/job/41436469385?pr=244

That is much too long for a CI action on a pull request.