Publish samplesheet to output directory

[Aratz]

This PR copies the samplesheet to the output directory at the beginning of the run.

Leaving this as draft for now as it needs to be merged after #163

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• 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>).
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.

[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: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[Copilot]

Pull Request Overview

This PR adds functionality to copy the input samplesheet to the output directory's pipeline_info folder at the start of the pipeline run, improving reproducibility by preserving the exact input configuration used.

Key Changes:

• Copies the samplesheet file to the output directory at pipeline initialization
• Updates test snapshots to include the samplesheet in expected outputs
• Documents the new output in the pipeline documentation

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
workflows/pixelator.nf	Adds file copy operation to publish samplesheet to pipeline_info directory
tests/pna.nf.test.snap	Updates test snapshots to include samplesheet file in expected outputs
tests/mpx.nf.test.snap	Updates test snapshots to include samplesheet file in expected outputs
docs/output.md	Documents the samplesheet as a new output artifact
CHANGELOG.md	Records the feature addition in the changelog

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