Update modules.config

[TCLamnidis]

• Removed enabled:true statements from publishDir directives.
• Added exclusion of versions.yml from modules that lacked a publishDir.pattern
• Moved preprocessing results into dedicated tool directories.
• Corrected publishDir for BAM filtering process (preprocessing -> bam_filtering)
• Minor formatting changes (indentation)

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• 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).

[TCLamnidis]

lints fine with nf-core/tools version 2.14.1 locally. I suspect the failed linting is to do with template merge #1095