Add support for CRAM, check contigs name

[LouisLeNezet]

Here we add support for CRAM file as input.
The contigs names are now check at workflow level for all input (bam and vcf).
Fix glimpse2 file naming.
Remove samples in one step with removing multiallelics records.
Publish only once the reference panel.
Moove samtools merge to BAM_REGION sbwf and fix renaming.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/phaseimpute branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core 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>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[atrigila]

Let's ask for an additional review to revise the new workflow.

[atrigila]

Great! Can you submit this updated module to nf-core modules as well? Then we can do the migration from local to nf-core modules.

[maxulysse]

I love it

[LouisLeNezet]

Ready to go