Fixing bug issues with SNR; quantms-utils -> quantms-rescoring

[ypriverol]

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[Copilot]

Pull Request Overview

This PR addresses bugs in the SNR processing by switching from quantms‑utils to quantms‑rescoring and updating related command parameters and container images.

• Updated container image references and command invocation in the spectrum2features module.
• Introduced a new configuration flag in the test DDA configuration file.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
modules/local/spectrum2features/main.nf	Updated container image and command parameters from quantms‑utils to quantms‑rescoring.
conf/test_dda_id.config	Added a new flag to enable SNR feature percolator testing.

Comments suppressed due to low confidence (1)

modules/local/spectrum2features/main.nf:25

• Ensure the updated command parameters for 'rescoring' (using '--mzml' instead of '--ms_path') match the rescoring CLI documentation to avoid unintended behavior.

rescoring spectrum2feature --mzml "${ms_file}" --idxml "${id_file}" --output "${id_file.baseName}_snr.idXML" 2>&1 | tee add_snr_feature.log

[Copilot]

[nitpick] Consider updating the usage or configuration documentation to explain the purpose of the new 'add_snr_feature_percolator' flag.