Merge pull request #1621 from nf-core/qualimap-performance-optimization

pinin4fjords · web-flow · commit a1188dcb659a · 2025-11-24T10:29:52.000Z
Optimize qualimap performance with multi-threaded name sorting
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ Special thanks to the following for their contributions to the release:
 
 - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
 - [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
+- [PR #1621](https://github.com/nf-core/rnaseq/pull/1621) - Optimize qualimap performance with multi-threaded name sorting
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 
diff --git a/modules/nf-core/qualimap/rnaseq/nextflow.config b/modules/nf-core/qualimap/rnaseq/nextflow.config
diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "BAM input for Salmon": {
         "content": [
-            139,
+            144,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -79,6 +79,9 @@
                 "SAMTOOLS_INDEX": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
@@ -958,7 +961,7 @@
     },
     "BAM input for RSEM": {
         "content": [
-            138,
+            143,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -1041,6 +1044,9 @@
                 "SAMTOOLS_INDEX": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: default": {
         "content": [
-            209,
+            214,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -199,6 +199,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: --featurecounts_group_type false": {
         "content": [
-            199,
+            204,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -196,6 +196,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -103,7 +103,7 @@
     },
     "Params: --aligner hisat2": {
         "content": [
-            200,
+            205,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -203,6 +203,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --min_mapped_reads 90": {
         "content": [
-            163,
+            166,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --remove_ribo_rna": {
         "content": [
-            220,
+            225,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap
@@ -102,7 +102,7 @@
     },
     "Params: default --use_sentieon_star": {
         "content": [
-            209,
+            214,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -199,6 +199,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --skip_trimming": {
         "content": [
-            199,
+            204,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -98,6 +98,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Params: --aligner star_rsem": {
         "content": [
-            207,
+            212,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.18
@@ -109,6 +109,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "--umi_dedup_tool 'umitools'": {
         "content": [
-            261,
+            266,
             {
                 "BEDTOOLS_GENOMECOV_FW": {
                     "bedtools": "2.31.1"
@@ -92,6 +92,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
@@ -1507,7 +1510,7 @@
     },
     "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
         "content": [
-            194,
+            199,
             {
                 "BEDTOOLS_GENOMECOV_FW": {
                     "bedtools": "2.31.1"
@@ -1601,6 +1604,9 @@
                 "SAMTOOLS_SORT": {
                     "samtools": 1.21
                 },
+                "SAMTOOLS_SORT_QUALIMAP": {
+                    "samtools": 1.21
+                },
                 "SAMTOOLS_STATS": {
                     "samtools": 1.21
                 },
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
@@ -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]})
