[FIX] Correct logic for linear deduplication

[HDash]

Fixes #293

The bug and its fix are all detailed in the issue above.

Additionally, handle case where an empty input (no alignments) is passed to LA dedup Python script.

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!
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• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
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• If necessary, also make a PR on the nf-core/cutandrun branch on the nf-core/test-datasets repository.
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• Make sure your code lints (nf-core lint).
  NA: PR change does not affect existing lint status
• 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.
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• Output Documentation in docs/output.md is updated.
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• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[Copilot]

Pull Request Overview

This PR fixes a logic error in linear deduplication where reads with the lowest MAPQ scores were being kept instead of the highest quality reads. The fix includes a version bump and changelog update to document the correction.

• Fixed logic error in linear deduplication functionality
• Updated version from 3.2.2 to 3.2.3
• Added changelog entry documenting the bug fix

Reviewed Changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated no comments.

File	Description
nextflow.config	Bumped version number from 3.2.2 to 3.2.3
CHANGELOG.md	Added new version entry documenting the deduplication logic fix

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[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @HDash,

It looks like this pull-request is has been made against the HDash/cutandrun master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the HDash/cutandrun dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[NathanSkene]

Important to get this approved / pulled. Until that's done, we cannot trust the resulting scores... which stops us from understanding what TIP-seq peaks are.