2.4.7 Patch

[jfy133]

Closes #983 and a broken conda environment

Tested by manually editing environment to bump the pygments to the minimal version as reported in teh error, and then linted with nf-core tools 1.9

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).

[github-actions]

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --config .github/markdownlint.yml --fix
  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

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[apeltzer]

LGTM!

[TCLamnidis]

@aidaanva was adamant that we should also bump MultiQC to fix a division by 0 error. Is there a reason why we don't? and if we do, maybe double check that the dependencies work with it 👀

[TCLamnidis]

partial approval. see my comment. I am fine either way, but if the latest MQC version fixes a bug in one of the modules, it seems like a good time to add that too.