gzip compression of temp fastq files and replaced nanofilt with chopper

[nick-youngblut]

• compression of temp fastq files
  • SPLIT_SEQ module
• replaced nanofilt with chopper
  • CHOPPER module

I haven't updated some of the extras (e.g., CHANGELOG), since I'm not sure how you want to structure them (e.g., what release version?).

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 - have you followed the pipeline conventions in the contribution docs
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• Make sure your code lints (nf-core pipelines lint).
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• 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

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[lianov]

@nick-youngblut : wanted to provide you a quick update here. We are doing some internal tests for the 1.2.0 release which will hopefully be out within the next couple of weeks pending our checks and the experience of some of our internal UAB users. We are leaving your PR for release 1.3.0 to minimize scope for 1.2.0. But as soon as we release 1.2.0 we will start looking at this PR. Again, thanks so much for the contribution, we think this is a great feature for scnanoseq. We will continue to keep you posted.

[nick-youngblut]

@lianov thanks for the update!
I've been trying to contribute to various open source bioinformatics codebases lately, given how quickly one can now work with AI coding tools (e.g., Claude, Cursor, Codex, etc). I hope this PR at least provides some guidance (for your LLM coder) to reduce temporary storage space.