diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 02d9b0f992b2..aab585ac4223 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -22,7 +22,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path("${prefix}.${file_type}.crai"),                      emit: crai,             optional: true
     tuple val(meta), path("${prefix}.unselected.${file_type}"),                emit: unselected,       optional: true
     tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"),     emit: unselected_index, optional: true
-    path  "versions.yml",                                                      emit: versions
+    tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -60,11 +60,6 @@ process SAMTOOLS_VIEW {
         -o ${output_file} \\
         $input \\
         $args2
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -95,10 +90,5 @@ process SAMTOOLS_VIEW {
     ${index}
     ${unselected}
     ${unselected_index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
index 3ebbdb891054..f56bf28ae256 100644
--- a/modules/nf-core/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -140,13 +140,29 @@ output:
           description: index for the "unselected" file
           pattern: "*.unselected.{csi,crai}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - samtools:
+          type: string
+          description: Name of the tool
+      - samtools --version | head -1 | sed -e "s/samtools //:
+          type: string
+          description: Version of samtools used
+
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
+  
 authors:
   - "@drpatelh"
   - "@joseespinosa"
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test
index d8551dd8c6bf..de57b8e36e83 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test
+++ b/modules/nf-core/samtools/view/tests/main.nf.test
@@ -29,13 +29,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") },
-                { assert snapshot(process.out.bai).match("bam_bai") },
-                { assert snapshot(process.out.crai).match("bam_crai") },
-                { assert snapshot(process.out.cram).match("bam_cram") },
-                { assert snapshot(process.out.csi).match("bam_csi") },
-                { assert snapshot(process.out.sam).match("bam_sam") },
-                { assert snapshot(process.out.versions).match("bam_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()}
             )
         }
     }
@@ -62,11 +56,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.bam[0][1]).name,
-                    file(process.out.csi[0][1]).name,
-                    process.out.versions).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
             )
         }
     }
@@ -93,10 +83,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.bam[0][1]).name,
-                    file(process.out.bai[0][1]).name,
-                    process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai"])).match()}
             )
         }
     }
@@ -124,13 +111,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.bam[0][1]).name,
-                    file(process.out.bai[0][1]).name,
-                    file(process.out.unselected[0][1]).name,
-                    file(process.out.unselected_index[0][1]).name,
-                    process.out.versions).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()}
             )
         }
     }
@@ -158,13 +139,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.cram[0][1]).name,
-                    file(process.out.crai[0][1]).name,
-                    file(process.out.unselected[0][1]).name,
-                    file(process.out.unselected_index[0][1]).name,
-                    process.out.versions).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index", "crai"])).match()}
             )
         }
     }
@@ -192,13 +167,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") },
-                { assert snapshot(process.out.bai).match("cram_bai") },
-                { assert snapshot(process.out.bam).match("cram_bam") },
-                { assert snapshot(process.out.crai).match("cram_crai") },
-                { assert snapshot(process.out.csi).match("cram_csi") },
-                { assert snapshot(process.out.sam).match("cram_sam") },
-                { assert snapshot(process.out.versions).match("cram_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cram"])).match()}
             )
         }
     }
@@ -228,13 +197,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") },
-                { assert snapshot(process.out.bai).match("cram_to_bam_bai") },
-                { assert snapshot(process.out.crai).match("cram_to_bam_crai") },
-                { assert snapshot(process.out.cram).match("cram_to_bam_cram") },
-                { assert snapshot(process.out.csi).match("cram_to_bam_csi") },
-                { assert snapshot(process.out.sam).match("cram_to_bam_sam") },
-                { assert snapshot(process.out.versions).match("cram_to_bam_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()}
             )
         }
     }
@@ -264,13 +227,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") },
-                { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") },
-                { assert snapshot(process.out.bai).match("cram_to_bam_index_bai") },
-                { assert snapshot(process.out.crai).match("cram_to_bam_index_crai") },
-                { assert snapshot(process.out.cram).match("cram_to_bam_index_cram") },
-                { assert snapshot(process.out.sam).match("cram_to_bam_index_sam") },
-                { assert snapshot(process.out.versions).match("cram_to_bam_index_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
             )
         }
     }
@@ -300,15 +257,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") },
-                { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") },
-                { assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") },
-                { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") },
-                { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") },
-                { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") },
-                { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") },
-                { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") },
-                { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()}
             )
         }
     }
@@ -336,13 +285,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") },
-                { assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") },
-                { assert snapshot(process.out.bai).match("bam_stub_bai") },
-                { assert snapshot(process.out.crai).match("bam_stub_crai") },
-                { assert snapshot(process.out.cram).match("bam_stub_cram") },
-                { assert snapshot(process.out.sam).match("bam_stub_sam") },
-                { assert snapshot(process.out.versions).match("bam_stub_versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()}
             )
         }
     }
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap
index 5ec65d62b31c..6ee160cd42ea 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap
@@ -1,244 +1,49 @@
 {
-    "bam_bam": {
-        "content": [
-            "test.bam"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:51.256068"
-    },
-    "bam_stub_bam": {
-        "content": [
-            "test.bam"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:32.065301"
-    },
-    "bam_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:51.258578"
-    },
-    "bam_stub_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:32.071284"
-    },
-    "bam_stub_versions": {
-        "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:20:28.366024"
-    },
-    "cram_to_bam_index_qname_csi": {
-        "content": [
-            "test.bam.csi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.325496"
-    },
-    "cram_to_bam_index_qname_unselected_csi": {
-        "content": [
-            "test.unselected.bam.csi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.328458"
-    },
-    "bam_csi": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:51.262882"
-    },
-    "cram_to_bam_index_bam": {
-        "content": [
-            "test.bam"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.95456"
-    },
-    "cram_to_bam_index_versions": {
-        "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:20:20.3853"
-    },
-    "bam_csi_index": {
-        "content": [
-            "test.bam",
-            "test.bam.csi",
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:19:54.889079"
-    },
-    "bam_versions": {
-        "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:19:51.017781"
-    },
-    "cram_crai_index_unselected - stub": {
+    "cram_to_bam_index": {
         "content": [
             {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
+                "bai": [
                     
                 ],
-                "5": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "6": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "7": [
+                "bam": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam"
                     ]
                 ],
-                "8": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-                ],
-                "bai": [
+                "crai": [
                     
                 ],
-                "bam": [
+                "cram": [
                     
                 ],
-                "crai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "cram": [
+                "csi": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam.csi"
                     ]
-                ],
-                "csi": [
-                    
                 ],
                 "sam": [
                     
                 ],
                 "unselected": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
                 ]
             }
         ],
@@ -246,79 +51,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:44.809515"
-    },
-    "bam_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:51.259774"
-    },
-    "bam_cram": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:51.261287"
-    },
-    "cram_sam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.502625"
-    },
-    "cram_versions": {
-        "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:20:12.471005"
-    },
-    "cram_to_bam_index_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.962863"
-    },
-    "cram_to_bam_index_qname_sam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.337634"
+        "timestamp": "2025-10-29T15:41:48.952660444"
     },
     "bam_csi_index - stub": {
         "content": [
@@ -360,7 +93,11 @@
                     
                 ],
                 "8": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "bai": [
                     
@@ -398,8 +135,12 @@
                 "unselected_index": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
@@ -407,94 +148,67 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:32.118817"
-    },
-    "cram_to_bam_index_csi": {
-        "content": [
-            "test.bam.csi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.958617"
-    },
-    "bam_bai_index": {
-        "content": [
-            "test.bam",
-            "test.bam.bai",
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T15:19:58.85102"
-    },
-    "cram_to_bam_index_cram": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.972288"
+        "timestamp": "2025-10-29T15:42:14.881335093"
     },
-    "bam_bai_index - stub": {
+    "bam_csi_index": {
         "content": [
             {
-                "0": [
+                "bai": [
+                    
+                ],
+                "bam": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam"
                     ]
                 ],
-                "1": [
+                "crai": [
                     
                 ],
-                "2": [
+                "cram": [
                     
                 ],
-                "3": [
+                "csi": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam.csi"
                     ]
                 ],
-                "4": [
-                    
-                ],
-                "5": [
+                "sam": [
                     
                 ],
-                "6": [
+                "unselected": [
                     
                 ],
-                "7": [
+                "unselected_index": [
                     
                 ],
-                "8": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-                ],
-                "bai": [
+                "versions_samtools": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
                     ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-10-29T15:40:50.701779393"
+    },
+    "cram_to_bam_index_qname": {
+        "content": [
+            {
+                "bai": [
+                    
                 ],
                 "bam": [
                     [
@@ -502,7 +216,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bam"
                     ]
                 ],
                 "crai": [
@@ -512,19 +226,41 @@
                     
                 ],
                 "csi": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.csi:md5,15d725bced7ececd45b4312b2af99a6b"
+                    ]
                 ],
                 "sam": [
                     
                 ],
                 "unselected": [
-                    
-                ],
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam"
+                    ]
+                ],
                 "unselected_index": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam.csi"
+                    ]
                 ],
-                "versions": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
@@ -532,297 +268,489 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:35.787886"
-    },
-    "cram_to_bam_sam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:04.999247"
-    },
-    "cram_to_bam_index_sam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.976457"
-    },
-    "cram_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.497581"
-    },
-    "cram_csi": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.50038"
-    },
-    "cram_to_bam_cram": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:04.992239"
-    },
-    "bam_stub_sam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:32.079529"
+        "timestamp": "2025-10-29T15:41:58.085628072"
     },
-    "cram_cram": {
-        "content": [
-            "test.cram"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.490286"
-    },
-    "cram_to_bam_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:04.989247"
-    },
-    "cram_to_bam_index_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:12.967681"
-    },
-    "cram_crai_index_unselected": {
+    "bam_bai_index_unselected": {
         "content": [
-            "test.cram",
-            "test.cram.crai",
-            "test.unselected.cram",
-            "test.unselected.cram.crai",
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
+            {
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam"
+                    ]
+                ],
+                "unselected_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.bam.csi"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:07.026136"
+        "timestamp": "2025-10-29T15:41:10.249194373"
     },
-    "cram_to_bam_index_qname_versions": {
+    "cram_crai_index_unselected - stub": {
         "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "unselected_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:24.609054"
+        "timestamp": "2025-10-29T15:42:39.3240134"
     },
-    "cram_to_bam_bam": {
+    "bam": {
         "content": [
-            "test.bam"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:04.982361"
-    },
-    "cram_to_bam_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:04.98601"
-    },
-    "cram_to_bam_versions": {
-        "content": [
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
+            {
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:16.51014"
-    },
-    "cram_bam": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.495512"
-    },
-    "bam_stub_cram": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:32.076908"
-    },
-    "cram_to_bam_index_qname_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.328458"
+        "timestamp": "2025-10-29T15:40:42.829284764"
     },
-    "cram_to_bam_index_qname_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.330789"
-    },
-    "cram_bai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:37:56.493129"
-    },
-    "bam_stub_crai": {
-        "content": [
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:32.074313"
-    },
-    "cram_to_bam_index_qname_bam": {
+    "bam_bai_index": {
         "content": [
-            "test.bam"
+            {
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-02-12T19:38:23.322874"
+        "timestamp": "2025-10-29T15:41:00.734899949"
     },
-    "bam_bai_index_unselected": {
+    "cram_to_bam": {
         "content": [
-            "test.bam",
-            "test.bam.bai",
-            "test.unselected.bam",
-            "test.unselected.bam.csi",
-            [
-                "versions.yml:md5,376bd183239f91c807210bfeb299d306"
-            ]
+            {
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:03.049076"
+        "timestamp": "2025-10-29T15:41:40.148480065"
     },
-    "cram_to_bam_index_qname_cram": {
+    "bam_bai_index - stub": {
         "content": [
-            [
-                
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    
+                ],
+                "8": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-02-12T19:38:23.333248"
+        "timestamp": "2025-10-29T15:42:22.748940869"
     },
-    "cram_to_bam_csi": {
+    "cram": {
         "content": [
-            [
-                
-            ]
+            {
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-02-12T19:38:04.995454"
+        "timestamp": "2025-10-29T15:41:30.602610389"
     },
     "bam_bai_index_uselected - stub": {
         "content": [
@@ -876,7 +804,11 @@
                     ]
                 ],
                 "8": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "bai": [
                     [
@@ -926,8 +858,12 @@
                         "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,376bd183239f91c807210bfeb299d306"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
@@ -935,38 +871,126 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T15:20:39.633146"
-    },
-    "cram_to_bam_index_qname_unselected": {
-        "content": [
-            "test.unselected.bam"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
-        },
-        "timestamp": "2024-02-12T19:38:23.322874"
+        "timestamp": "2025-10-29T15:42:31.1133801"
     },
-    "bam_sam": {
+    "cram_crai_index_unselected": {
         "content": [
-            [
-                
-            ]
+            {
+                "bai": [
+                    
+                ],
+                "bam": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram.crai"
+                    ]
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cram:md5,9b6eeca8f6b4b744297ae7cc87c031a4"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram"
+                    ]
+                ],
+                "unselected_index": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.unselected.cram.crai"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-02-12T19:37:51.264651"
+        "timestamp": "2025-10-29T15:49:09.738258028"
     },
-    "bam_stub_csi": {
+    "bam_stub": {
         "content": [
-            "test.bam.csi"
+            {
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bam.csi"
+                    ]
+                ],
+                "sam": [
+                    
+                ],
+                "unselected": [
+                    
+                ],
+                "unselected_index": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_VIEW",
+                        "samtools",
+                        "1.22.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-02-12T19:38:32.068596"
+        "timestamp": "2025-10-29T15:42:06.108061867"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_split_by_region/main.nf b/subworkflows/nf-core/bam_split_by_region/main.nf
index 71b4d01c4e37..50442c767d5e 100644
--- a/subworkflows/nf-core/bam_split_by_region/main.nf
+++ b/subworkflows/nf-core/bam_split_by_region/main.nf
@@ -46,7 +46,6 @@ workflow BAM_SPLIT_BY_REGION {
 
     // The specified region is put into ext.args2 from the meta. See nextflow.config of the subworkflow.
     SAMTOOLS_VIEW(ch_bam_for_splitting, [[],[]], [], [])
-    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
 
     //
     // Index the output bams
diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
index a7d769116dcb..0f4d217d7143 100644
--- a/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
+++ b/subworkflows/nf-core/bam_subsampledepth_samtools/main.nf
@@ -40,7 +40,6 @@ workflow BAM_SUBSAMPLEDEPTH_SAMTOOLS {
         [],
         []
     )
-    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
 
     // Aggregate bam and index
     ch_bam_subsampled = SAMTOOLS_VIEW.out.bam.mix(SAMTOOLS_VIEW.out.cram, SAMTOOLS_VIEW.out.sam)
diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap
index 91cfb02a009f..4ff5aad204db 100644
--- a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap
@@ -42,7 +42,6 @@
                 ],
                 "1": [
                     "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb",
-                    "versions.yml:md5,d90a2995d11e3c2a4a8b99799fb86fb6",
                     "versions.yml:md5,eeb0a1f1cb18d25b5c98bf1f408302a7"
                 ],
                 "bam_subsampled": [
@@ -85,7 +84,6 @@
                 ],
                 "versions": [
                     "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb",
-                    "versions.yml:md5,d90a2995d11e3c2a4a8b99799fb86fb6",
                     "versions.yml:md5,eeb0a1f1cb18d25b5c98bf1f408302a7"
                 ]
             },
@@ -128,6 +126,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:08:42.206943"
+        "timestamp": "2025-10-29T15:26:28.531547254"
     }
 }
\ No newline at end of file