Remove unused outputs from PREPARE_PAIR process

[paliocha]

Problem

PREPARE_PAIR declares 5 outputs but only pair_id is used downstream:

output:
    tuple val(tissue), val("${sp1}_${sp2}"), emit: pair_id  // ✅ USED
    path "*.RData", emit: data_files        // ❌ UNUSED
    path "*.txt", emit: expr_files          // ❌ UNUSED
    path "config.R", emit: config_file      // ❌ UNUSED
    path "pair_stats.tsv", emit: stats_file, optional: true  // ❌ UNUSED

Why this matters:

• Unnecessary file staging overhead
• Confuses pipeline data flow
• Wastes disk I/O

Solution

Remove unused output declarations. If files are needed later, include them in the tuple:

output:
    tuple val(tissue), val("${sp1}_${sp2}"), emit: pair_id

OR if intermediate files are needed:

output:
    tuple val(tissue), val("${sp1}_${sp2}"), path("*.RData"), emit: pair_data

Priority: Medium
Effort: Low
Note: This will invalidate PREPARE_PAIR cache