Fix shapeit5 hash divergence

[LouisLeNezet]

PR checklist

This PR fix the reproducibility issue with singularity on some machine.
After a lot of debugging this seemed to come from the vcf.gz format and .tbi index that when given to SHAPEIT5_phase_common would result in different phase for some individuals for just a few position but still throwing off the variants md5sum result.

To solve this without adding an extra module, VCFLIB_VCFFIXUP module was updated to output any vcf format + index.
This removed one module necessary and stabilised the hash.

See https://nfcore.slack.com/archives/C04PPJLT1T3/p1781099185452859 for the full rubber ducking.

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