Fix shuffled NetMHCpan/NetMHCIIpan allele labels in merged/best_allele output (fixes #358)

[jonasscheid]

Description

Fixes #358.

MERGE_PREDICTIONS reconstructed which allele each NetMHC output column belonged to from sorted(meta.alleles). This is wrong whenever the pipeline's sort order diverges from the predictor's output column order: the rank/BA values (tied to their column position) stay correct, but the allele labels — and the downstream best_allele — get shuffled. Two real triggers:

• NetMHCIIpan (class II): it writes allele columns sorted in its own allele-name format, which strips the : (DPB1*10:01 → DPB11001). Combined with variable-width first fields (10 vs 107), the : (ASCII 58, sorts after digits) flips the order relative to the pipeline's mhcgnomes sort.
• NetMHCpan (class I): a stray space in a samplesheet allele (e.g. ...;C*07:01; C*07:04) makes ' C*07:04' sort first (space = ASCII 32), rotating the whole column→allele mapping by one.

The fix reads the authoritative allele order from the xls header row (each predictor labels every allele block there) instead of assuming sorted(meta.alleles). This is robust to both triggers above and also fixes a latent misalignment when some requested alleles are unsupported by the predictor.

Verified end-to-end with real NetMHCIIpan 4.3 (divergent DPB1*10:01 / DPB1*107:01) and real NetMHCpan 4.2 (the reported spaced-allele case): every allele now maps to its correct rank and best_allele is correct.

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[nf-core-bot]

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