Use bcftools/isec nf-core module for computing VCF intersection between multiple callers

[maxibor]

This PR replaces the python calling of bcftools isec in the isec_vcfs.py script by the nf-core modules of bcftools isec.
The main changes are:

• Retrieving tool names using nextflow operators and passing them in the meta map
• Retrieving the number of VCF per sample in nf, and passing it in the meta map.
• Adding bcftools/isec nf-core modules for computing VCF intersections for samples having been called using multiple callers.
• Adding a local module for processing VCF from samples having been called using a single caller.

This PR would close issue #28

This is work done at the Barcelona 2025 nf-core hackathon together with @eolaniru

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated.

[famosab]

Please run

pre-commit run --all-files

[famosab]

nf-test test --update-snapshot --profile test,docker tests/default.nf.test

[famosab]

@YussAb I already saw this with the template pr that the md5sums are not stable. I think we need to figure out why and if we can stabilize or assert differently.

[famosab]

@maxibor in #51 I had to add some sorting to the isec_vcfs script. Do you think there is a way to include the same logic here? :)