Add improved liftover pipeline (using bcftools +liftover)

[ainefairbrother]

Description

In response to ticket #6088.

This PR re-implements the Remapping Nextflow pipeline using bcftools +liftover (freeseek/score plug-in) instead of CrossMap.

• modules/bcftools_liftover.nf — new module that mirrors the old crossmap.nf (input: *.vcf, outputs: *.unmap, _report.txt).
  -bcftools +liftover runs inside the docker image fairbrot/bcftools-liftover:latest (bcftools 1.20 + plug-ins).
• Added README.md with usage, container notes, and sample command lines.

Use case

bcftools +liftover performs better on a number of metrics than CrossMap - see ticket comments for detailed benchmarking info summarised from the manuscript.

Testing

I benchmarked the older Remapping pipeline (using CrossMap) against this one.

• Input: ClinVar VCF
• Liftover: GRCh38 > T2T

Report coming out of this pipeline (liftover):

#ID	Assembly	Failed	Total	Percentage
T2T_CHM13_v2	GCA_009914755.4	2099	3503922	.05

Report coming out of Remapping pipeline

#ID	Assembly	Failed	Total	Percentage
T2T_CHM13_v2	GCA_009914755.4	35905	3503922	1.02

As you can see, Remapping failed to lift over 35,905 variants, whereas liftover only failed to lift over 2,099 variants.