diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0eb8458bc..5cde9cf6e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release
 - [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds
 - [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build
+- [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility
 
 ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16
 
diff --git a/modules.json b/modules.json
index 7bea6205b..7f889aeec 100644
--- a/modules.json
+++ b/modules.json
@@ -215,7 +215,8 @@
                     "sortmerna": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
+                        "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
+                        "patch": "modules/nf-core/sortmerna/sortmerna.diff"
                     },
                     "star/align": {
                         "branch": "master",
diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml
index fab44081f..75d586704 100644
--- a/modules/nf-core/sortmerna/environment.yml
+++ b/modules/nf-core/sortmerna/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sortmerna=4.3.6
+  - seqera::sortmerna=4.3.7
diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf
index 7c17e500c..6850dc1d7 100644
--- a/modules/nf-core/sortmerna/main.nf
+++ b/modules/nf-core/sortmerna/main.nf
@@ -4,8 +4,8 @@ process SORTMERNA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' :
-        'biocontainers/sortmerna:4.3.6--h9ee0642_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' :
+        'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff
new file mode 100644
index 000000000..5c3b1775d
--- /dev/null
+++ b/modules/nf-core/sortmerna/sortmerna.diff
@@ -0,0 +1,539 @@
+Changes in module 'nf-core/sortmerna'
+Changes in 'sortmerna/main.nf':
+--- modules/nf-core/sortmerna/main.nf
++++ modules/nf-core/sortmerna/main.nf
+@@ -4,8 +4,8 @@
+ 
+     conda "${moduleDir}/environment.yml"
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' :
+-        'biocontainers/sortmerna:4.3.6--h9ee0642_0' }"
++        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' :
++        'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }"
+ 
+     input:
+     tuple val(meta), path(reads)
+
+Changes in 'sortmerna/environment.yml':
+--- modules/nf-core/sortmerna/environment.yml
++++ modules/nf-core/sortmerna/environment.yml
+@@ -2,4 +2,4 @@
+   - conda-forge
+   - bioconda
+ dependencies:
+-  - bioconda::sortmerna=4.3.6
++  - seqera::sortmerna=4.3.7
+
+'modules/nf-core/sortmerna/meta.yml' is unchanged
+'modules/nf-core/sortmerna/nextflow.config' was created
+Changes in 'sortmerna/tests/main.nf.test.snap':
+--- modules/nf-core/sortmerna/tests/main.nf.test.snap
++++ modules/nf-core/sortmerna/tests/main.nf.test.snap
+@@ -2,14 +2,14 @@
+     "versions_paired_end_stub": {
+         "content": [
+             [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:27:11.223149"
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:01.533875274"
+     },
+     "index_paired_end_stub": {
+         "content": [
+@@ -25,48 +25,22 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T14:24:25.384097178"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:01.450465678"
+     },
+     "versions_paired_end": {
+         "content": [
+             [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:27:04.517155"
+-    },
+-    "versions_single_end_stub": {
+-        "content": [
+-            [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-01T12:10:35.228450189"
+-    },
+-    "sarscov2 single_end_match": {
+-        "content": [
+-            [
+-                "test.non_rRNA.fastq.gz",
+-                "test.sortmerna.log",
+-                "{id=test}"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:28:23.20327"
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:48.811712136"
+     },
+     "index_only_stub": {
+         "content": [
+@@ -82,44 +56,79 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:00:47.128504164"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:38:56.554562414"
++    },
++    "sarscov2 single_end_match": {
++        "content": [
++            [
++                "test.non_rRNA.fastq.gz",
++                "test.sortmerna.log",
++                "{id=test}"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:09.015863183"
++    },
++    "versions_single_end_stub": {
++        "content": [
++            [
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:28.573618474"
+     },
+     "index_single_end_premade_index": {
+         "content": [
+             [
+-                [
+-                    {
+-                        "id": "test2"
+-                    },
+-                    [
+-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+-                    ]
+-                ]
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:01:53.832643452"
++                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
++                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
++                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:14.159307146"
+     },
+     "versions_single_end_premade_index": {
+         "content": [
+             [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:01:53.902154982"
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:14.269803641"
++    },
++    "sarscov2 indexing only": {
++        "content": [
++            [
++                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
++                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
++                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7"
++            ],
++            [
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:38:39.794977786"
+     },
+     "sarscov2 paired_end-for_stub_match": {
+         "content": [
+@@ -133,32 +142,24 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:28:56.063579"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:01.365507281"
+     },
+     "index_paired_end": {
+         "content": [
+             [
+-                [
+-                    {
+-                        "id": "test2"
+-                    },
+-                    [
+-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+-                    ]
+-                ]
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T14:24:14.272659781"
++                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
++                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
++                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:48.72523749"
+     },
+     "sarscov2 single_end_premade_index_match_stub": {
+         "content": [
+@@ -169,10 +170,10 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:05:01.913287272"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:28.87594616"
+     },
+     "sarscov2 single_end-for_stub_match": {
+         "content": [
+@@ -183,10 +184,10 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:28:29.197913"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:28.458349619"
+     },
+     "sarscov2 paired_end_match": {
+         "content": [
+@@ -200,46 +201,46 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-07T12:28:49.914992"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:48.667990373"
+     },
+     "versions_single_end": {
+         "content": [
+             [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T14:36:27.14244294"
+-    },
+-    "versions_index_only": {
+-        "content": [
+-            [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:00:35.609161481"
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:09.110655329"
+     },
+     "versions_single_end_premade_index_stub": {
+         "content": [
+             [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:05:02.059858431"
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:29.097777821"
++    },
++    "versions_index_only_stub": {
++        "content": [
++            [
++                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:38:56.592840673"
+     },
+     "index_single_end_stub": {
+         "content": [
+@@ -255,22 +256,10 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T14:23:58.068772508"
+-    },
+-    "versions_index_only_stub": {
+-        "content": [
+-            [
+-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:00:47.169402699"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:28.516407836"
+     },
+     "index_single_end_premade_index_stub": {
+         "content": [
+@@ -286,54 +275,24 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:05:01.953316205"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:28.988436085"
+     },
+     "index_single_end": {
+         "content": [
+             [
+-                [
+-                    {
+-                        "id": "test2"
+-                    },
+-                    [
+-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+-                    ]
+-                ]
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T14:36:26.88061978"
+-    },
+-    "index_index_only": {
+-        "content": [
+-            [
+-                [
+-                    {
+-                        "id": "test2"
+-                    },
+-                    [
+-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
+-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
+-                    ]
+-                ]
+-            ]
+-        ],
+-        "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:00:35.34089252"
++                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
++                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
++                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7"
++            ]
++        ],
++        "meta": {
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:39:09.050777261"
+     },
+     "sarscov2 single_end_premade_index_match": {
+         "content": [
+@@ -344,9 +303,9 @@
+             ]
+         ],
+         "meta": {
+-            "nf-test": "0.8.4",
+-            "nextflow": "23.10.1"
+-        },
+-        "timestamp": "2024-02-26T15:01:53.797737296"
++            "nf-test": "0.9.0",
++            "nextflow": "24.04.4"
++        },
++        "timestamp": "2024-10-22T10:40:14.075100849"
+     }
+ }
+Changes in 'sortmerna/tests/main.nf.test':
+--- modules/nf-core/sortmerna/tests/main.nf.test
++++ modules/nf-core/sortmerna/tests/main.nf.test
+@@ -27,8 +27,10 @@
+             assertAll(
+                 { assert process.success },
+                 { assert ! process.out.reads },
+-                { assert snapshot(process.out.index).match("index_index_only") },
+-                { assert snapshot(process.out.versions).match("versions_index_only") }
++                { assert snapshot(
++                    file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") },
++                    process.out.versions                   
++                ).match() },
+             )
+         }
+ 
+@@ -92,7 +94,7 @@
+                         ).sort()
+                     ).match("sarscov2 single_end_match")
+                 },
+-                { assert snapshot(process.out.index).match("index_single_end") },
++                { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_single_end") },
+                 { assert snapshot(process.out.versions).match("versions_single_end") }
+             )
+         }
+@@ -170,7 +172,7 @@
+                         ).sort()
+                     ).match("sarscov2 paired_end_match")
+                 },
+-                { assert snapshot(process.out.index).match("index_paired_end") },
++                { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_paired_end") },
+                 { assert snapshot(process.out.versions).match("versions_paired_end") }
+             )
+         }
+@@ -265,7 +267,7 @@
+                         ).sort()
+                     ).match("sarscov2 single_end_premade_index_match")
+                 },
+-                { assert snapshot(process.out.index).match("index_single_end_premade_index") },
++                { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }).match("index_single_end_premade_index") },
+                 { assert snapshot(process.out.versions).match("versions_single_end_premade_index") }
+             )
+         }
+
+'modules/nf-core/sortmerna/tests/tags.yml' is unchanged
+'modules/nf-core/sortmerna/tests/premade_index.config' is unchanged
+'modules/nf-core/sortmerna/tests/indexing_only.config' is unchanged
+************************************************************
diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test
index 4388cda0c..4e1ced131 100644
--- a/modules/nf-core/sortmerna/tests/main.nf.test
+++ b/modules/nf-core/sortmerna/tests/main.nf.test
@@ -3,6 +3,9 @@ nextflow_process {
     name "Test Process SORTMERNA"
     script "../main.nf"
     process "SORTMERNA"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sortmerna"
 
     test("sarscov2 indexing only") {
  
@@ -21,11 +24,17 @@ nextflow_process {
         }
 
         then {
+            def index_files = file(process.out.index[0][1]).listFiles()
+                .findAll { !it.name.endsWith('.stats') }
+                .sort { a, b -> a.name <=> b.name }
+            
             assertAll(
                 { assert process.success },
                 { assert ! process.out.reads },
-                { assert snapshot(process.out.index).match("index_index_only") },
-                { assert snapshot(process.out.versions).match("versions_index_only") }
+                { assert snapshot(
+                    index_files,
+                    process.out.versions                   
+                ).match() },
             )
         }
 
@@ -76,6 +85,10 @@ nextflow_process {
         }
 
         then {
+            def index_files = file(process.out.index[0][1]).listFiles()
+                .findAll { !it.name.endsWith('.stats') }
+                .sort { a, b -> a.name <=> b.name }
+            
             assertAll(
                 { assert process.success },
                 { assert process.out.reads },
@@ -89,7 +102,7 @@ nextflow_process {
                         ).sort()
                     ).match("sarscov2 single_end_match")
                 },
-                { assert snapshot(process.out.index).match("index_single_end") },
+                { assert snapshot(index_files).match("index_single_end") },
                 { assert snapshot(process.out.versions).match("versions_single_end") }
             )
         }
@@ -154,6 +167,10 @@ nextflow_process {
         }
 
         then {
+            def index_files = file(process.out.index[0][1]).listFiles()
+                .findAll { !it.name.endsWith('.stats') }
+                .sort { a, b -> a.name <=> b.name }
+
             assertAll(
                 { assert process.success },
                 { assert process.out.reads },
@@ -167,7 +184,7 @@ nextflow_process {
                         ).sort()
                     ).match("sarscov2 paired_end_match")
                 },
-                { assert snapshot(process.out.index).match("index_paired_end") },
+                { assert snapshot(index_files).match("index_paired_end") },
                 { assert snapshot(process.out.versions).match("versions_paired_end") }
             )
         }
@@ -249,6 +266,10 @@ nextflow_process {
         }
 
         then {
+            def index_files = file(process.out.index[0][1]).listFiles()
+                .findAll { !it.name.endsWith('.stats') }
+                .sort { a, b -> a.name <=> b.name }
+
             assertAll(
                 { assert process.success },
                 { assert process.out.reads },
@@ -262,7 +283,7 @@ nextflow_process {
                         ).sort()
                     ).match("sarscov2 single_end_premade_index_match")
                 },
-                { assert snapshot(process.out.index).match("index_single_end_premade_index") },
+                { assert snapshot(index_files).match("index_single_end_premade_index") },
                 { assert snapshot(process.out.versions).match("versions_single_end_premade_index") }
             )
         }
diff --git a/modules/nf-core/sortmerna/tests/main.nf.test.snap b/modules/nf-core/sortmerna/tests/main.nf.test.snap
index 86e84733b..07c2e3294 100644
--- a/modules/nf-core/sortmerna/tests/main.nf.test.snap
+++ b/modules/nf-core/sortmerna/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "versions_paired_end_stub": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:27:11.223149"
+        "timestamp": "2024-10-22T10:40:01.533875274"
     },
     "index_paired_end_stub": {
         "content": [
@@ -25,34 +25,41 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T14:24:25.384097178"
+        "timestamp": "2024-10-22T10:40:01.450465678"
     },
     "versions_paired_end": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:27:04.517155"
+        "timestamp": "2024-10-22T10:39:48.811712136"
     },
-    "versions_single_end_stub": {
+    "index_only_stub": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                [
+                    {
+                        "id": "test2"
+                    },
+                    [
+                        
+                    ]
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-01T12:10:35.228450189"
+        "timestamp": "2024-10-22T10:38:56.554562414"
     },
     "sarscov2 single_end_match": {
         "content": [
@@ -63,63 +70,65 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:28:23.20327"
+        "timestamp": "2024-10-22T10:39:09.015863183"
     },
-    "index_only_stub": {
+    "versions_single_end_stub": {
         "content": [
             [
-                [
-                    {
-                        "id": "test2"
-                    },
-                    [
-                        
-                    ]
-                ]
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:00:47.128504164"
+        "timestamp": "2024-10-22T10:39:28.573618474"
     },
     "index_single_end_premade_index": {
         "content": [
             [
-                [
-                    {
-                        "id": "test2"
-                    },
-                    [
-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
-                    ]
-                ]
+                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:01:53.832643452"
+        "timestamp": "2024-10-22T12:02:37.578808801"
     },
     "versions_single_end_premade_index": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-22T10:40:14.269803641"
+    },
+    "sarscov2 indexing only": {
+        "content": [
+            [
+                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef"
+            ],
+            [
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:01:53.902154982"
+        "timestamp": "2024-10-22T11:59:11.705138075"
     },
     "sarscov2 paired_end-for_stub_match": {
         "content": [
@@ -133,32 +142,24 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:28:56.063579"
+        "timestamp": "2024-10-22T10:40:01.365507281"
     },
     "index_paired_end": {
         "content": [
             [
-                [
-                    {
-                        "id": "test2"
-                    },
-                    [
-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
-                    ]
-                ]
+                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T14:24:14.272659781"
+        "timestamp": "2024-10-22T12:01:29.664107565"
     },
     "sarscov2 single_end_premade_index_match_stub": {
         "content": [
@@ -169,10 +170,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:05:01.913287272"
+        "timestamp": "2024-10-22T10:40:28.87594616"
     },
     "sarscov2 single_end-for_stub_match": {
         "content": [
@@ -183,10 +184,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:28:29.197913"
+        "timestamp": "2024-10-22T10:39:28.458349619"
     },
     "sarscov2 paired_end_match": {
         "content": [
@@ -200,46 +201,46 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-07T12:28:49.914992"
+        "timestamp": "2024-10-22T10:39:48.667990373"
     },
     "versions_single_end": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T14:36:27.14244294"
+        "timestamp": "2024-10-22T10:39:09.110655329"
     },
-    "versions_index_only": {
+    "versions_single_end_premade_index_stub": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:00:35.609161481"
+        "timestamp": "2024-10-22T10:40:29.097777821"
     },
-    "versions_single_end_premade_index_stub": {
+    "versions_index_only_stub": {
         "content": [
             [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
+                "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:05:02.059858431"
+        "timestamp": "2024-10-22T10:38:56.592840673"
     },
     "index_single_end_stub": {
         "content": [
@@ -255,22 +256,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T14:23:58.068772508"
-    },
-    "versions_index_only_stub": {
-        "content": [
-            [
-                "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-26T15:00:47.169402699"
+        "timestamp": "2024-10-22T10:39:28.516407836"
     },
     "index_single_end_premade_index_stub": {
         "content": [
@@ -286,54 +275,24 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:05:01.953316205"
+        "timestamp": "2024-10-22T10:40:28.988436085"
     },
     "index_single_end": {
         "content": [
             [
-                [
-                    {
-                        "id": "test2"
-                    },
-                    [
-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
-                    ]
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-26T14:36:26.88061978"
-    },
-    "index_index_only": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test2"
-                    },
-                    [
-                        "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
-                        "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
-                        "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef",
-                        "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c"
-                    ]
-                ]
+                "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a",
+                "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7",
+                "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:00:35.34089252"
+        "timestamp": "2024-10-22T12:00:30.580004574"
     },
     "sarscov2 single_end_premade_index_match": {
         "content": [
@@ -344,9 +303,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-26T15:01:53.797737296"
+        "timestamp": "2024-10-22T10:40:14.075100849"
     }
 }
\ No newline at end of file
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
index 8dedc7693..789571cfb 100644
--- a/tests/remove_ribo_rna.nf.test.snap
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -102,10 +102,10 @@
                     "bioconductor-summarizedexperiment": "1.32.0"
                 },
                 "SORTMERNA": {
-                    "sortmerna": "4.3.6"
+                    "sortmerna": "4.3.7"
                 },
                 "SORTMERNA_INDEX": {
-                    "sortmerna": "4.3.6"
+                    "sortmerna": "4.3.7"
                 },
                 "STAR_ALIGN": {
                     "star": "2.7.11b",
@@ -1386,7 +1386,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-21T20:02:26.804814864"
+        "timestamp": "2024-10-22T12:24:58.795267716"
     },
     "Params: --remove_ribo_rna - stub": {
         "content": [
@@ -1420,7 +1420,7 @@
                     "gunzip": 1.1
                 },
                 "SORTMERNA_INDEX": {
-                    "sortmerna": "4.3.6"
+                    "sortmerna": "4.3.7"
                 },
                 "STAR_GENOMEGENERATE": {
                     "star": "2.7.11b",
@@ -1482,6 +1482,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-21T20:03:16.221160765"
+        "timestamp": "2024-10-22T12:26:10.797017969"
     }
 }
\ No newline at end of file