Copy quantification GTF to project-level results root (once, not per-sample)

[mtinti]

Motivation

• Ensure the processed annotation GTF used for quantification is copied once to the project-level results directory rather than being duplicated into each sample folder so the canonical annotation is easy to find.

Description

• Move the GTF copy out of the per-sample copy_results flow and into the project-level copy_results_all rule in rules/results.smk so the file is staged once in the results root.
• Add gtf_file = config["processing_gtf_file"] and results_root = get_results_path() to the copy_results_all rule params and invoke cp {params.gtf_file} {params.results_root}/ during that rule's shell step.
• Remove the per-sample GTF copy and the per-sample completion message for the GTF so it is no longer placed into each sample directory.
• Keep logging of the GTF copy in copy_results_all to record the action in logs/copy_results_all.log.

Testing

• No automated tests were run for this change.

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Codex Task