diff --git a/CHANGELOG.md b/CHANGELOG.md
index 10e88e4b8..b6338c1c4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,10 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Credits
 
+Special thanks to the following for their contributions to the release:
+
+- [sisterdot](https://github.com/sisterdot)
+
 ### Enhancements and fixes
 
 - [PR #1640](https://github.com/nf-core/rnaseq/pull/1640) - Bump version after release 3.22.0
 - [PR #1641](https://github.com/nf-core/rnaseq/pull/1641) - Add arm-based CI tests and fix arm-related issues
+- [PR #1645](https://github.com/nf-core/rnaseq/pull/1645) - Fix BAM CSI index access error with UMI deduplication ([#1643](https://github.com/nf-core/rnaseq/issues/1643))
 - [PR #1642](https://github.com/nf-core/rnaseq/pull/1642) - Add long format to rsem merge
 
 ## [[3.22.0](https://github.com/nf-core/rnaseq/releases/tag/3.22.0)] - 2025-11-26
diff --git a/modules.json b/modules.json
index 87d4bd1fa..d7963d8ad 100644
--- a/modules.json
+++ b/modules.json
@@ -77,7 +77,7 @@
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
+                        "git_sha": "5ec0e05ebe154cf1325de4c8ae07cdff1a197b06",
                         "installed_by": ["fastq_align_hisat2"],
                         "patch": "modules/nf-core/hisat2/align/hisat2-align.diff"
                     },
diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff
index 74551638b..946fa9615 100644
--- a/modules/nf-core/hisat2/align/hisat2-align.diff
+++ b/modules/nf-core/hisat2/align/hisat2-align.diff
@@ -11,7 +11,7 @@ Changes in 'hisat2/align/main.nf':
 -        def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
 +        def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
          """
-         INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
+         INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
          hisat2 \\
 @@ -56,7 +56,7 @@
          END_VERSIONS
@@ -20,7 +20,7 @@ Changes in 'hisat2/align/main.nf':
 -        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
 +        def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
          """
-         INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
+         INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
          hisat2 \\
 @@ -91,7 +91,7 @@
  
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
index 1487bcf7b..d2166579a 100644
--- a/modules/nf-core/hisat2/align/main.nf
+++ b/modules/nf-core/hisat2/align/main.nf
@@ -36,7 +36,7 @@ process HISAT2_ALIGN {
     if (meta.single_end) {
         def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         """
-        INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
+        INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
         hisat2 \\
             -x \$INDEX \\
             -U $reads \\
@@ -58,7 +58,7 @@ process HISAT2_ALIGN {
     } else {
         def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         """
-        INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
+        INDEX=`find -L ./ -name "*.1.ht2*" | sed 's/\\.1.ht2.*\$//'`
         hisat2 \\
             -x \$INDEX \\
             -1 ${reads[0]} \\
diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml
index 3416c87aa..8a466b646 100644
--- a/modules/nf-core/hisat2/align/meta.yml
+++ b/modules/nf-core/hisat2/align/meta.yml
@@ -26,6 +26,7 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
   - - meta2:
         type: map
         description: |
@@ -35,6 +36,7 @@ input:
         type: file
         description: HISAT2 genome index file
         pattern: "*.ht2"
+        ontologies: []
   - - meta3:
         type: map
         description: |
@@ -44,9 +46,10 @@ input:
         type: file
         description: Splices sites in gtf file
         pattern: "*.{txt}"
+        ontologies: []
 output:
-  - bam:
-      - meta:
+  bam:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -55,8 +58,9 @@ output:
           type: file
           description: Output BAM file containing read alignments
           pattern: "*.{bam}"
-  - summary:
-      - meta:
+          ontologies: []
+  summary:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -65,8 +69,9 @@ output:
           type: file
           description: Alignment log
           pattern: "*.log"
-  - fastq:
-      - meta:
+          ontologies: []
+  fastq:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -75,11 +80,15 @@ output:
           type: file
           description: Output FastQ file
           pattern: "*fastq.gz"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@ntoda03"
   - "@ramprasadn"
diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap
index 69928644b..158ef53dc 100644
--- a/tests/bam_input.nf.test.snap
+++ b/tests/bam_input.nf.test.snap
@@ -1300,6 +1300,8 @@
                 "rsem/WT_REP2.transcript.bam",
                 "rsem/rsem.merged.gene_counts.tsv",
                 "rsem/rsem.merged.gene_tpm.tsv",
+                "rsem/rsem.merged.genes_long.tsv",
+                "rsem/rsem.merged.isoforms_long.tsv",
                 "rsem/rsem.merged.transcript_counts.tsv",
                 "rsem/rsem.merged.transcript_tpm.tsv",
                 "samtools",
@@ -1819,6 +1821,8 @@
                 "WT_REP2.transcript.bam:md5,a5f965731a3fd6e523f4960d7d462f97",
                 "rsem.merged.gene_counts.tsv:md5,47a75de167a1b72d3a20789df389a3f7",
                 "rsem.merged.gene_tpm.tsv:md5,18a6dd460737434f6da1c17c1dc8aafa",
+                "rsem.merged.genes_long.tsv:md5,24767425e5d9d914ed0b1eca431182ac",
+                "rsem.merged.isoforms_long.tsv:md5,1363e166497e4574793a9f4704841767",
                 "rsem.merged.transcript_counts.tsv:md5,d3a4fa1f3bde89ee9d30114af2db3b48",
                 "rsem.merged.transcript_tpm.tsv:md5,efa563d0402cae35b96380592d147a72",
                 "RAP1_IAA_30M_REP1.sorted.bam.bai:md5,4460948fc194ba7c7fe7ad92e68132a0",
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
index 399938a39..18a53941c 100644
--- a/tests/star_rsem.nf.test.snap
+++ b/tests/star_rsem.nf.test.snap
@@ -986,6 +986,8 @@
                 "star_rsem/qualimap/WT_REP2/rnaseq_qc_results.txt",
                 "star_rsem/rsem.merged.gene_counts.tsv",
                 "star_rsem/rsem.merged.gene_tpm.tsv",
+                "star_rsem/rsem.merged.genes_long.tsv",
+                "star_rsem/rsem.merged.isoforms_long.tsv",
                 "star_rsem/rsem.merged.transcript_counts.tsv",
                 "star_rsem/rsem.merged.transcript_tpm.tsv",
                 "star_rsem/rseqc",
@@ -1306,6 +1308,8 @@
                 "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846",
                 "rsem.merged.gene_counts.tsv:md5,990cdaf5071c9bfd3d2d99296feb68f3",
                 "rsem.merged.gene_tpm.tsv:md5,349f2184161d6b269a0f5c4da1dee07a",
+                "rsem.merged.genes_long.tsv:md5,42e9a0220b0e3a505d7b59df279ce89a",
+                "rsem.merged.isoforms_long.tsv:md5,8c6f65b49b920e48caf93dc04e1a546c",
                 "rsem.merged.transcript_counts.tsv:md5,3ca2bb5c22438e0bd104c9d052bc8241",
                 "rsem.merged.transcript_tpm.tsv:md5,f59e35398f30d49875e41bcc03d082ed",
                 "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de",
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index b61312ad3..317525506 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -253,7 +253,7 @@ workflow RNASEQ {
 
             ch_genome_bam        = BAM_DEDUP_UMI_STAR.out.bam
             ch_transcriptome_bam = BAM_DEDUP_UMI_STAR.out.transcriptome_bam
-            ch_genome_bam_index  = params.bam_csi_index ? BAM_DEDUP_UMI_STAR.out.csi : BAM_DEDUP_UMI_STAR.out.bai
+            ch_genome_bam_index  = BAM_DEDUP_UMI_STAR.out.bai
             ch_versions          = ch_versions.mix(BAM_DEDUP_UMI_STAR.out.versions)
 
             ch_multiqc_files = ch_multiqc_files
@@ -359,7 +359,7 @@ workflow RNASEQ {
             )
 
             ch_genome_bam        = BAM_DEDUP_UMI_HISAT2.out.bam
-            ch_genome_bam_index  = params.bam_csi_index ? BAM_DEDUP_UMI_HISAT2.out.csi : BAM_DEDUP_UMI_HISAT2.out.bai
+            ch_genome_bam_index  = BAM_DEDUP_UMI_HISAT2.out.bai
             ch_versions          = ch_versions.mix(BAM_DEDUP_UMI_HISAT2.out.versions)
 
             ch_multiqc_files = ch_multiqc_files