Modules update

[muffato]

Hi,

The most important thing I want to fix is the container used for samtools. I noticed it was staphb/samtools:1.22.1 for a few modules, all patched from nf-core. Perhaps there was no biocontainer at the time ?
We have to favour standard containers built on BioConda: first biocontainers, and falling back to Seqera containers.
nf-core modules all use biocontainers/samtools:1.22.1 so I've decided to update those, and whilst at it, I updated all modules.

After this, only 2 .diff files remain.

The test profile runs fine. The test_full profile should complete this morning.

I had to modify a few sub-workflows to not gather the versions channel, including one from sanger-tol I believe. I think nf-core lint may complain. I'll double-check and may open a PR in sanger-tol/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
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).

[sainsachiko]

This look fine to me, assuming all the test pass.

[muffato]

All tests passed