move bcftools and tabix to nf-core

[kubranarci]

I am transforming local modules with bcftools and tabix to standard nf-core modules

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!
• 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/variantbenchmarking branch on the nf-core/test-datasets repository.
• 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>).
• 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).

[kubranarci]

I know it seems like big change

• local bcftools rename_chr and reheader are deleted and we start to use nf-core bcftools/annotate and bcftools/reheader
• local bgzip_tabix is deleted, we switch to use tabix/tabix and tabix/bgziptabix instead
• wittyer needed a fix to enable running with singularity
• bcftools tools are updated to latest using topic channels for version
• tabix tools are updated to latest using topic channels for version
• the changes in subworkflows reflecting those changes.

[georgiakes]

No worries ☺️ . Looks good to me.

[kubranarci]

Thank you!