nf-core · maxulysse · Aug 31, 2026 · Aug 31, 2026 · Sep 1, 2026 · Sep 1, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1902](https://github.com/nf-core/rnaseq/pull/1902) - Update `bam_stringtie_merge` and StringTie modules ([nf-core/modules#12661](https://github.com/nf-core/modules/pull/12661)), allowing runs where all samples fail `--min_mapped_reads` to complete with skipped-sample warnings instead of failing an empty StringTie merge ([#1901](https://github.com/nf-core/rnaseq/issues/1901))
 - [PR #1907](https://github.com/nf-core/rnaseq/pull/1907) - Update `fastq_qc_trim_filter_setstrandedness` ([nf-core/modules#12745](https://github.com/nf-core/modules/pull/12745)), fixing a crash in Salmon auto-strandedness inference when no `--fasta` is supplied (e.g. kallisto-only pseudoalignment runs)
 - [PR #1911](https://github.com/nf-core/rnaseq/pull/1911) - Copy instead of symlink index files in `STAR_GENOMEPARAMS_UPGRADE`, fixing broken/missing index files on object-storage-backed work directories (e.g. Azure Batch via azcopy) that can't represent symlinks
+- [PR #1913](https://github.com/nf-core/rnaseq/pull/1913) - Update HISAT2 modules
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 
@@ -76,11 +77,17 @@ Special thanks to the following for their contributions to the release:
 
 ### Software dependencies
 
-| Dependency      | Old version | New version |
-| --------------- | ----------- | ----------- |
-| `trim-galore`   | 0.6.10      | 2.1.0       |
-| `gawk`          |             | 5.3.1       |
-| `STAR` (legacy) | 2.6.1d      |             |
+| Dependency                  | Old version | New version |
+| --------------------------- | ----------- | ----------- |
+| `trim-galore`               | 0.6.10      | 2.1.0       |
+| `gawk`                      |             | 5.3.1       |
+| `STAR` (legacy)             | 2.6.1d      |             |
+| `hisat2/align`              | 2.2.1       | 2.2.3       |
+| --`samtools`                | 1.20        | 1.24        |
+| `hisat2/build`              | 2.2.1       | 2.2.3       |
+| --`samtools`                | 1.20        |             |
+| `hisat2/extractsplicesites` | 2.2.1       | 2.2.3       |
+| --`samtools`                | 1.20        | 1.24        |
 
 `gawk` is added as a dependency of the new `STAR_GENOMEPARAMS_UPGRADE` local module. The `STAR` (legacy) row reflects removal of the parallel STAR 2.6.1d build that ran alongside the default aligner for legacy iGenomes indices; the pipeline-default STAR is unchanged.
 

diff --git a/conf/arm.config b/conf/arm.config
@@ -93,15 +93,15 @@ process {
     }
 
     withName: 'HISAT2_ALIGN' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3c/3c7546a094e92519aed723d67cb7419a0fb220ff605db9cdd08813dacae301a3/data' : 'community.wave.seqera.io/library/hisat2_samtools:487d2cbbcebf2256' }
     }
 
     withName: 'HISAT2_BUILD' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e4bec1a1694b5aa3fea4fb8f965e36f6499ff488fe501574a8e0da2932ce817/data' : 'community.wave.seqera.io/library/hisat2:2.2.3--87f2824b626e6fde' }
     }
 
     withName: 'HISAT2_EXTRACTSPLICESITES' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95a04506094435ef9cbd94b479d5cd713cd1d106d5e5718bf4410686c3d19f15/data' : 'community.wave.seqera.io/library/hisat2_samtools:aaedc5f7a0ece7e8' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3c/3c7546a094e92519aed723d67cb7419a0fb220ff605db9cdd08813dacae301a3/data' : 'community.wave.seqera.io/library/hisat2_samtools:487d2cbbcebf2256' }
     }
 
     withName: 'KALLISTO_INDEX' {

diff --git a/conf/modules/align_hisat2.config b/conf/modules/align_hisat2.config
@@ -12,6 +12,13 @@ process {
             if (seqPlatform) argsList << "--rg PL:${seqPlatform}"
             if (seqCenter) argsList << "--rg CN:${seqCenter}"
 
+            // Strandedness
+            if (meta.strandedness == 'forward') {
+                argsList << (meta.single_end ? '--rna-strandness F' : '--rna-strandness FR')
+            } else if (meta.strandedness == 'reverse') {
+                argsList << (meta.single_end ? '--rna-strandness R' : '--rna-strandness RF')
+            }
+
             argsList.join(' ')
         }
         publishDir = [

diff --git a/main.nf b/main.nf
@@ -112,7 +112,8 @@ workflow NFCORE_RNASEQ {
         params.skip_pseudo_alignment,
         params.use_sentieon_star,
         params.use_parabricks_star,
-        isStarIndexLegacy() ?: false
+        isStarIndexLegacy() ?: false,
+        params.hisat2_build_memory
     )
 
     // Check if contigs in genome fasta file > 512 Mbp

diff --git a/modules.json b/modules.json
@@ -106,17 +106,17 @@
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "cebe21bbd158c15c8fab172e37cfe97a239f4b77",
+                        "git_sha": "7ff2dbaefb93fdd3825b7bff1d86d2f3c7e946f5",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "hisat2/build": {
                         "branch": "master",
-                        "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c",
+                        "git_sha": "7ff2dbaefb93fdd3825b7bff1d86d2f3c7e946f5",
                         "installed_by": ["modules"]
                     },
                     "hisat2/extractsplicesites": {
                         "branch": "master",
-                        "git_sha": "004e773fc35ebd24063ca4cbef057c94a24208aa",
+                        "git_sha": "22b467cf44542d7e16b1410c5dbd5982c9545f27",
                         "installed_by": ["modules"]
                     },
                     "kallisto/index": {

diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml