REFACTOR: Improve dna2protein bottleneck

[m-huertasp]

Summary

This PR optimizes the DNA2PROTEINMAPPING step by reducing its bottleneck. Previously, the pipeline executed multiple serial requests to Ensembl REST APIs (roughly 2× the number of genes in a panel), which frequently led to rate-limiting blocks and significant latency for large panels.

Based on suggestions from @FerriolCalvet , the individual calls were replaced with a bulk-retrieval strategy. We now download the full GFF annotation via FTP and process it locally.

Main Changes

• New logic: Replaced multiple REST API calls with a single FTP parsing of the Ensembl GFF. The document is not downloaded but filtered on the fly and briefly kept in memory until transformation into a dataframe.
• Refactor: Updated downstream functions to handle DataFrames instead of the JSON objects previously returned by the API.
• Flexibility: Linked the Ensembl release version to the vep_cache_version Nextflow parameter, allowing users to specify the genomic release dynamically.
• Documentation: Added docstrings and internal comments to explain the new and old parsing logic.

closes #229

[Copilot]

Pull request overview

This PR refactors the DNA2PROTEINMAPPING step to reduce Ensembl REST API bottlenecks by switching to a bulk retrieval + local parsing approach using the Ensembl GFF3 (fetched from Ensembl FTP), and threads an Ensembl release parameter into the mapping step.

Changes:

• Add an optional --ensembl-release argument wiring in the Nextflow module.
• Replace transcript/exon/CDS retrieval from Ensembl REST with streaming download + local filtering of Ensembl GFF3 and DataFrame-based downstream processing.
• Refactor exon-ID assignment and related plotting/coverage helpers.

Reviewed changes

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

File	Description
modules/local/dna2protein/main.nf	Adds --ensembl-release argument passing to the mapping script.
bin/panels_computedna2protein.py	Implements GFF3 streaming retrieval/parsing and refactors coordinate mapping, exon lookup, and coverage plotting.

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[FerriolCalvet]

all good! great Marta!

[FerriolCalvet]

very minor changes from testing

[FerriolCalvet]

when testing this file needs to have more memory, particularly for bigger panels, add the process_medium_high_memory label and then merge

[m-huertasp]

This will not be added in this branch but in ferriol-updates branch.