Optimize qualimap performance with multi-threaded name sorting

Pre-sort BAM files by read name using samtools with multi-threading before
running qualimap rnaseq. This reduces qualimap execution time by >50%
(from ~85 min to <40 min) by offloading the single-threaded sorting to
the multi-threaded samtools sort with the -n flag, then passing the
sorted BAM to qualimap with the --sorted flag.

Resolves #1356

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: pinin4fjords

modules/nf-core/qualimap/rnaseq/nextflow.config

@@ -47,6 +47,7 @@ include { MULTIQC                    } from '../../modules/nf-core/multiqc'
 include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW          } from '../../modules/nf-core/bedtools/genomecov'
 include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV         } from '../../modules/nf-core/bedtools/genomecov'
 include { SAMTOOLS_INDEX                                       } from '../../modules/nf-core/samtools/index'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT_QUALIMAP              } from '../../modules/nf-core/samtools/sort'
 
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -539,8 +540,15 @@ workflow RNASEQ {
     //
     if (!params.skip_qc) {
         if (!params.skip_qualimap) {
-            QUALIMAP_RNASEQ (
+            // Sort BAM by name for qualimap (performance optimization)
+            SAMTOOLS_SORT_QUALIMAP (
                 ch_genome_bam,
+                ch_fasta.map { [ [:], it ] }
+            )
+            ch_versions = ch_versions.mix(SAMTOOLS_SORT_QUALIMAP.out.versions.first())
+
+            QUALIMAP_RNASEQ (
+                SAMTOOLS_SORT_QUALIMAP.out.bam,
                 ch_gtf.map { [ [:], it ] }
             )
             ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_RNASEQ.out.results.collect{it[1]})