Patch Release: 2.3.3

[jfy133]

Release for patch 2.3.3

Added

• #349 - Added option enabling platypus formatted output of pmdtools misincorporation frequencies.

Fixed

• #719 - Fix filename for bam output of mapdamage_rescaling
• #707 - Fix typo in UnifiedGenotyper IndelRealigner command
• Fixed some Java tools not following process memory specifications
• Updated template to nf-core/tools 1.13.2
• #711 - Fix conditional execution preventing multivcfanalyze to run
• #714 - Fixes bug in nuc contamination by upgrading to latest MultiQC v1.10.1 bugfix release

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
• 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]

The linter assumes any - at the start of a line is a markdown bullet. That should not be applied within code blocks...
usage.md is in need of some TLC (many more instances than I suggested changes for). Preferably, we should fix the linter, then checkout and re-lint usage (assuming all changes are linting related).

[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

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

[TCLamnidis]

Happy for merging after the small linting typos are corrected. In my suggestions I changed - for — for parenthetical sentences, which the linters should leave alone in the future. 🤞