Patch Release 2.4.3

[jfy133]

Patch release 2.4.3

Fixed

• #828 Improved error message if required metagenomic screening parameters not set correctly
• #836 Remove deprecated parameters from test profiles
• #838 Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
• #843 Re-add direct piping of AdapterRemovalFixPrefix to pigz
• #844 Fixed reference masking prior to pmdtools
• #845 Updates parameter documention to specify -s preseq parameter also applies to lc_extrap
• #851 Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
• Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
• #857 Corrected samtools fastq flag to retain read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
• #858 Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting)

Dependencies

• #829 Bumped sequencetools: 1.4.0.5 -> 1.5.2
• Bumped MultiQC: 1.11 -> 1.12 (for run-time optimisation and tool citation information)

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] 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.
• [x] Make sure your code lints (nf-core lint .).
• [x] Ensure the test suite passes (nextflow run . -profile test,docker).
• [x] Usage Documentation in docs/usage.md is updated.
• [x] Output Documentation in docs/output.md is updated.
• [x] CHANGELOG.md is updated.
• [x] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

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 :+1:

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!