chore: update modules

[HomoPolyethylen]

This PR updates several modules and subworkflows.

Modules:

• bcftools/filter updated
• bcftools/norm updated
• tabix/... replaced with htslib/bgziptabix
  • tabix/tabix removed
  • tabix/bgziptabix removed
  • htslib/bgziptabix added
• multiqc updated
• pcgr/getref updated
• untar updated

Subworkflows:

• utils_nfcore_pipeline updated
• utils_nfschema_plugin updated

closes #99

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/variantprioritization 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).

[HomoPolyethylen]

I am not sure what to put in the changelog. just a simple "updated modules and subworkflows" in the changed section? or the specific changes in the depedencies section? since modules often don't have versioning (right?) should I use the git hashes from modules.json?

[famosab]

"updated modules and subworkflows" in the changed section?
this

and if the version is increased from modules then add it to the dependencies

For Example
bcftools 1.22 to 1.23.1

then we need to make sure that if these updated tools are used in local modules that there the version is also updated so we have the same version for one tool across the whole pipeline :)

[HomoPolyethylen]

and if the version is increased from modules then add it to the dependencies

For Example bcftools 1.22 to 1.23.1

that is concerning the core tool version right? not the nf-core module "wrapper"? they are versioned by git hashes (in modules.json), right?

then we need to make sure that if these updated tools are used in local modules that there the version is also updated so we have the same version for one tool across the whole pipeline :)

right, that sounds good. bcftools v1.22 is used in local modules intersect/vcf and reformat/vcf according to the conda env. so should we hold back on that update for now?

[famosab]

that is concerning the core tool version right? not the nf-core module "wrapper"? they are versioned by git hashes (in modules.json), right?

Yes, I think we can omit the git hashes in the CHANGELOG. If someone wants to really investigate they can look at the changes from a PR in the modules.json. We only care about tool versioning in that regard!

should we hold back on that update for now?

If you want you can simply add the tool update for the local modules to this PR. Let me know if you need guidance on anything regarding that :)

[famosab]

Nice work, i would just adapt the local modules to the new syntax (see proposed changes) and update the docs then we can merge this :)