Add xengsort contamination removal support

[xinghansun]

Description

Add xengsort as an additional contamination removal option in nf-core/sarek (follow-up to #1578 and the nf-core Hackathon project sarek-remove-genome-contaminants proposed by @apsteinberg).

What changed

• Add new modules: xengsort index and xengsort classify.
• Wire xengsort index through prepare_genome and classify through fastq_preprocess_gatk.
• Add new params and schema entries:
  • xengsort_host_fasta
  • xengsort_index
  • xengsort_nobjects
  • xengsort_kmersize
  • save_xengsort_reads
• Add xengsort tests and update snapshots.
• Update docs (README.md, docs/output.md).
• Sync ro-crate-metadata.json with updated docs.

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/sarek 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).

Validation run

• nf-test test tests/xengsort.nf.test --profile test, docker
• nf-test test modules/local/xengsort/index/tests/main.nf.test --profile docker
• nf-test test modules/local/xengsort/classify/tests/main.nf.test --profile docker
• nf-test test subworkflows/local/prepare_genome/tests/xengsort.nf.test --profile test, docker
• nf-core pipelines lint

Note

The CI test failures seem to be related to a SENTIEON license issue (likely due to missing or invalid license configuration in the CI environment).

[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.