Add methurator tool

[edogiuili]

In this PR, I add methurator as an additional QC tool for both the Bismark and bwa-meth subworkflows.

Methurator cannot currently be used with the TAPS/bwa-mem subworkflow because it relies on MethylDackel to extract CpG methylation information from BAM files.

Methurator is a Python package designed to estimate CpG sequencing saturation in DNA methylation sequencing data. It complements Preseq by estimating the number of sequencing reads required to achieve coverage of at least N CpGs with a minimum read depth of r. Because the estimator is based on a frequency-of-frequencies matrix derived from methylation count files, it can also be used to estimate library complexity for RRBS datasets.

Notes

• Methurator currently does not generate version YAML files. Instead, it outputs a topic channel, following the latest nf-core guidelines.
• Methurator v2.1.1 (the version used in this PR) does not yet have MultiQC support. A corresponding MultiQC PR has already been opened: Update methurator module MultiQC/MultiQC#3479.
• The fasta_index_methylseq lint test currently fails because I had to introduce a new methurator boolean parameter to trigger generation of the FASTA.FAI index. This index is required by Methurator due to its dependency on MethylDackel.

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/methylseq 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[edogiuili]

Tests 6,7,8,9 and 10 (and 3 only for conda profile) fail but I haven't changed them or anything related to their workflows. Might be that these tests were already failing?