diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml
index 9090f218834..5fd59cd2918 100644
--- a/modules/nf-core/bowtie2/align/environment.yml
+++ b/modules/nf-core/bowtie2/align/environment.yml
@@ -2,6 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bowtie2=2.5.2
+  - bioconda::bowtie2=2.5.4
   - bioconda::samtools=1.18
   - conda-forge::pigz=2.6
diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
index 809525ad36c..f683eb79c85 100644
--- a/modules/nf-core/bowtie2/align/main.nf
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -4,8 +4,8 @@ process BOWTIE2_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' :
-        'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' }"
+        'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :
+        'community.wave.seqera.io/library/bowtie2_samtools_pigz:8bde63944b003030' }"
 
     input:
     tuple val(meta) , path(reads)
diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test
index 0de5950fee6..89efa5c4b9b 100644
--- a/modules/nf-core/bowtie2/align/tests/main.nf.test
+++ b/modules/nf-core/bowtie2/align/tests/main.nf.test
@@ -35,7 +35,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -81,7 +81,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -90,7 +90,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    file(process.out.sam[0][1]).readLines()[0..4],
+                    file(process.out.sam[0][1]).readLines()[4..10],
                     process.out.log,
                     process.out.fastq,
                     process.out.versions
@@ -127,7 +127,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -136,7 +136,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    file(process.out.sam[0][1]).readLines()[0..4],
+                    file(process.out.sam[0][1]).readLines()[4..10],
                     process.out.log,
                     process.out.fastq,
                     process.out.versions
@@ -172,7 +172,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -220,7 +220,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -268,7 +268,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -314,7 +314,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -363,7 +363,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -411,7 +411,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -456,7 +456,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -553,7 +553,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
@@ -600,7 +600,7 @@ nextflow_process {
                 input[1] = BOWTIE2_BUILD.out.index
                 input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
                 input[3] = false //save_unaligned
-                input[4] = false //sort
+                input[4] = true //sort
                 """
             }
         }
diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap
index 028e7da6898..ea804909964 100644
--- a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap
@@ -15,23 +15,25 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:19:25.337323"
+        "timestamp": "2024-10-28T12:48:20.606057273"
     },
     "sarscov2 - fastq, index, fasta, false, false - sam2": {
         "content": [
             [
-                "ERR5069949.2151832\t16\tMT192765.1\t17453\t42\t150M\t*\t0\t0\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA<EEEEEEAEEEAEAAAAEEEEEEEEEAAAEE<EEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:150\tYT:Z:UU",
-                "ERR5069949.576388\t16\tMT192765.1\t5798\t42\t77M\t*\t0\t0\tGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT\tEA/AEEE/<EEEEEEEEEEEAA<EEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEE6/EEEAEEEEEEEEEA6AAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:77\tYT:Z:UU",
-                "ERR5069949.501486\t16\tMT192765.1\t5423\t42\t146M\t*\t0\t0\tTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTAC\tEAAAAEAEEEE6E<AEEEEEEEE<EEEEEEAAEE/EEEEEE/<EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:146\tYT:Z:UU",
-                "ERR5069949.1331889\t0\tMT192765.1\t13010\t42\t132M\t*\t0\t0\tGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG\tA/AAAEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEE/EEEEE<AEAEEEEE/EAEAEEE/AEEEEEEEEEEEEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEA<EE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:132\tYT:Z:UU",
-                "ERR5069949.2161340\t0\tMT192765.1\t17482\t42\t80M\t*\t0\t0\tAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT\tA/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<<EE</E/E\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:80\tYT:Z:UU"
+                "ERR5069949.29668\t16\tMT192765.1\t267\t42\t89M\t*\t0\t0\tCCTTGTCCCTGGTTACAACTAGAAACCACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAG\tE////6/E/EE/EE/<<///6EEE/////<AAA<A<A6AE/E/AE6A/EAEEEAEEEAEEEEEA/AEAE<EEEAEEE////6EEAA/AA\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:14T4G5A63\tYT:Z:UU",
+                "ERR5069949.114870\t0\tMT192765.1\t643\t42\t150M\t*\t0\t0\tAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAAC\tAAAAA/EAEEEEEEAEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEAEAEAEEAEEEEEEEEEEEEEEEEAEAA<EE</AAEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEAEEA<AEEEEEEA<<AAE<EEEEEAE<AAEAAAEAEE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:150\tYT:Z:UU",
+                "ERR5069949.147998\t16\tMT192765.1\t919\t42\t94M\t*\t0\t0\tTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGC\tEE<EEE//A/EEE/A</E<AEAE<EEEA<6EE/EEE/A/EAEAE<//EEEE/EEE6EEE/E/EE/EEE/EEAAEEEEEEEEEEEEEEAEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:94\tYT:Z:UU",
+                "ERR5069949.155944\t16\tMT192765.1\t1023\t42\t150M\t*\t0\t0\tTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCACTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCC\tEA<EA/<A/6A/AEA/6/66/AAAEAEEE/EEA/6AAAAAAEE</AAEEEEAAEEEAA/EEE//A/EEEEE/AE/EEE6AEEEE/A/EAEEEEE/EEAEEEAE/AEA66AEEEEEEEEE<AEEEAEEEEEEEEE6EEEEEEEAEEAAAAA\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:62C87\tYT:Z:UU",
+                "ERR5069949.184542\t0\tMT192765.1\t1055\t42\t151M\t*\t0\t0\tTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACAAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCTCCAAATGAATGCAACCAAATGTG\tAAAAAEEEEE/EA/E/EEE/EEAEE/E/EE/EEEE//AEE/E/EEE//EEE/</E/EE<<//EE/EE<EEEEEAE/E/EAAEEEAEAEE<E</EEEE/E//E<<<///E<//A<AE</<AEEEAAE///EE</EE//AA///<E</A<AEA\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:60C66A23\tYT:Z:UU",
+                "ERR5069949.169513\t0\tMT192765.1\t1098\t42\t92M\t*\t0\t0\tAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE6EEEE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:92\tYT:Z:UU",
+                "ERR5069949.257821\t16\tMT192765.1\t2834\t42\t139M\t*\t0\t0\tCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA\tA/AE<EE<EA</EAEAAA<AEEAEE/A/E<<E</E</EEEAAE/EE<E/EEEAEEEEEEE/AEEEEEEEEEEE/EEEE<EEEE/EE/EAEEE6EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:139\tYT:Z:UU"
             ],
             [
                 [
@@ -46,14 +48,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T12:31:40.337129939"
+        "timestamp": "2024-10-29T15:41:03.10995099"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true, true - cram": {
         "content": [
@@ -82,14 +84,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T12:58:55.482166476"
+        "timestamp": "2024-10-28T12:46:23.771955104"
     },
     "sarscov2 - fastq, index, fasta, true, false - bam": {
         "content": [
@@ -107,14 +109,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:19:55.741244"
+        "timestamp": "2024-10-28T12:48:59.016760556"
     },
     "sarscov2 - fastq, large_index, fasta, false, false - bam": {
         "content": [
@@ -132,14 +134,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:19:09.604979"
+        "timestamp": "2024-10-28T12:48:03.15737256"
     },
     "sarscov2 - fastq, index, fasta, false, true - bam": {
         "content": [
@@ -157,14 +159,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:18:22.547322"
+        "timestamp": "2024-10-28T12:47:13.41871986"
     },
     "sarscov2 - fastq, index, fasta, true, false - stub": {
         "content": [
@@ -175,14 +177,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:02:09.557518106"
+        "timestamp": "2024-10-28T12:49:42.090798629"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, false, false - bam": {
         "content": [
@@ -200,14 +202,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:18:38.78064"
+        "timestamp": "2024-10-28T12:47:26.78995535"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, false, false - stub": {
         "content": [
@@ -218,23 +220,25 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:20:26.047111"
+        "timestamp": "2024-10-28T12:49:28.417201351"
     },
     "sarscov2 - fastq, index, fasta, false, false - sam": {
         "content": [
             [
-                "ERR5069949.2151832\t16\tMT192765.1\t17453\t42\t150M\t*\t0\t0\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA<EEEEEEAEEEAEAAAAEEEEEEEEEAAAEE<EEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:150\tYT:Z:UU",
-                "ERR5069949.576388\t16\tMT192765.1\t5798\t42\t77M\t*\t0\t0\tGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT\tEA/AEEE/<EEEEEEEEEEEAA<EEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEE6/EEEAEEEEEEEEEA6AAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:77\tYT:Z:UU",
-                "ERR5069949.501486\t16\tMT192765.1\t5423\t42\t146M\t*\t0\t0\tTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTAC\tEAAAAEAEEEE6E<AEEEEEEEE<EEEEEEAAEE/EEEEEE/<EEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:146\tYT:Z:UU",
-                "ERR5069949.1331889\t0\tMT192765.1\t13010\t42\t132M\t*\t0\t0\tGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG\tA/AAAEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEE/EEEEE<AEAEEEEE/EAEAEEE/AEEEEEEEEEEEEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEA<EE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:132\tYT:Z:UU",
-                "ERR5069949.2161340\t0\tMT192765.1\t17482\t42\t80M\t*\t0\t0\tAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT\tA/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<<EE</E/E\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:80\tYT:Z:UU"
+                "ERR5069949.29668\t16\tMT192765.1\t267\t42\t89M\t*\t0\t0\tCCTTGTCCCTGGTTACAACTAGAAACCACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAG\tE////6/E/EE/EE/<<///6EEE/////<AAA<A<A6AE/E/AE6A/EAEEEAEEEAEEEEEA/AEAE<EEEAEEE////6EEAA/AA\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:14T4G5A63\tYT:Z:UU",
+                "ERR5069949.114870\t0\tMT192765.1\t643\t42\t150M\t*\t0\t0\tAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAAC\tAAAAA/EAEEEEEEAEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEAEAEAEEAEEEEEEEEEEEEEEEEAEAA<EE</AAEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEAEEA<AEEEEEEA<<AAE<EEEEEAE<AAEAAAEAEE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:150\tYT:Z:UU",
+                "ERR5069949.147998\t16\tMT192765.1\t919\t42\t94M\t*\t0\t0\tTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGC\tEE<EEE//A/EEE/A</E<AEAE<EEEA<6EE/EEE/A/EAEAE<//EEEE/EEE6EEE/E/EE/EEE/EEAAEEEEEEEEEEEEEEAEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:94\tYT:Z:UU",
+                "ERR5069949.155944\t16\tMT192765.1\t1023\t42\t150M\t*\t0\t0\tTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCACTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCC\tEA<EA/<A/6A/AEA/6/66/AAAEAEEE/EEA/6AAAAAAEE</AAEEEEAAEEEAA/EEE//A/EEEEE/AE/EEE6AEEEE/A/EAEEEEE/EEAEEEAE/AEA66AEEEEEEEEE<AEEEAEEEEEEEEE6EEEEEEEAEEAAAAA\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:62C87\tYT:Z:UU",
+                "ERR5069949.184542\t0\tMT192765.1\t1055\t42\t151M\t*\t0\t0\tTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACAAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCTCCAAATGAATGCAACCAAATGTG\tAAAAAEEEEE/EA/E/EEE/EEAEE/E/EE/EEEE//AEE/E/EEE//EEE/</E/EE<<//EE/EE<EEEEEAE/E/EAAEEEAEAEE<E</EEEE/E//E<<<///E<//A<AE</<AEEEAAE///EE</EE//AA///<E</A<AEA\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:60C66A23\tYT:Z:UU",
+                "ERR5069949.169513\t0\tMT192765.1\t1098\t42\t92M\t*\t0\t0\tAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE6EEEE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:92\tYT:Z:UU",
+                "ERR5069949.257821\t16\tMT192765.1\t2834\t42\t139M\t*\t0\t0\tCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA\tA/AE<EE<EA</EAEAAA<AEEAEE/A/E<<E</E</EEEAAE/EE<E/EEEAEEEEEEE/AEEEEEEEEEEE/EEEE<EEEE/EE/EAEEE6EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:139\tYT:Z:UU"
             ],
             [
                 [
@@ -249,14 +253,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T12:31:26.668053751"
+        "timestamp": "2024-10-29T15:40:54.33025496"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, true, false - bam": {
         "content": [
@@ -274,14 +278,14 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:19:40.606135"
+        "timestamp": "2024-10-28T12:48:42.495832835"
     },
     "sarscov2 - [fastq1, fastq2], index, fasta, false, true - bam": {
         "content": [
@@ -299,13 +303,13 @@
                 
             ],
             [
-                "versions.yml:md5,01d18ab035146ea790e9a0f70adb758f"
+                "versions.yml:md5,0034ff5d2b1c356b2208601e9647e055"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T13:18:54.194648"
+        "timestamp": "2024-10-28T12:47:48.370652703"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml
index e590f7ce326..027c88d08c6 100644
--- a/modules/nf-core/bowtie2/build/environment.yml
+++ b/modules/nf-core/bowtie2/build/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bowtie2=2.5.2
+  - bioconda::bowtie2=2.5.4
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 9e2e0e5e2cc..49fd148f063 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -4,8 +4,8 @@ process BOWTIE2_BUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bowtie2:2.5.2--py39h6fed5c7_0' :
-        'biocontainers/bowtie2:2.5.2--py39h6fed5c7_0' }"
+        'https://depot.galaxyproject.org/singularity/bowtie2:2.5.4--h7071971_4' :
+        'biocontainers/bowtie2:2.5.4--h7071971_4' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
index 6875e021398..389b94bdc06 100644
--- a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
+++ b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
                 ],
                 "index": [
                     [
@@ -36,10 +36,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,1df11e9b82891527271c889c880d3974"
+                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
                 ]
             }
         ],
-        "timestamp": "2023-11-23T11:51:01.107681997"
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-28T12:31:51.909007545"
     }
 }
\ No newline at end of file