Fix: fetch sra metadata retraction module

[gp201]

This pull request fixes a bug where an SRA sample that is not retracted was being assigned a retraction date.
It also includes minor updates to improve code clarity and maintain consistency across the pipeline. The main changes are a switch from shell to script for process execution, variable renaming for clarity, and minor formatting improvements. The version number has also been incremented.

Fix

• Add assertions enforcing SRA retraction consistency (retracted => has date; not retracted => no date)

General improvements and maintenance:

• Changed process execution from shell to script in the SRATOOLS_PREFETCH process for better compatibility and maintainability (modules/nf-core/sratools/prefetch/main.nf).
• Updated pipeline version from 1.5.1 to 1.5.2 in nextflow.config.

Code clarity and formatting:

• Renamed the unused lambda parameter from sra to _sra in the FLUSRA workflow to indicate it is not used (workflows/flusra.nf).

[Copilot]

Pull Request Overview

This pull request fixes a bug where SRA samples that are not retracted were incorrectly being assigned retraction dates, and includes minor maintenance improvements for code clarity and consistency.

• Fixed SRA retraction module bug and added assertions for retraction consistency validation
• Changed process execution method from shell to script for better compatibility
• Updated pipeline version and improved code formatting

Reviewed Changes

Copilot reviewed 3 out of 5 changed files in this pull request and generated no comments.

File	Description
workflows/flusra.nf	Renamed unused lambda parameter and improved formatting of filter operations
nextflow.config	Incremented pipeline version from 1.5.1 to 1.5.2
modules/nf-core/sratools/prefetch/main.nf	Changed process execution from shell to script

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