From 5c131dc50dcf96f3e1bbdda4650478988fa5c362 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 15:25:52 +0100
Subject: [PATCH 01/10] feat: update samtools sort module with version topic
 support

---
 modules/nf-core/samtools/sort/main.nf         |  14 +-
 modules/nf-core/samtools/sort/meta.yml        |  28 +-
 .../nf-core/samtools/sort/tests/main.nf.test  |  22 +-
 .../samtools/sort/tests/main.nf.test.snap     | 382 ++++++++++++------
 4 files changed, 281 insertions(+), 165 deletions(-)

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index d4bd5a32715a..d0b82510f34d 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -19,8 +19,8 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("${prefix}.${extension}.crai"),   emit: crai, optional: true
     tuple val(meta), path("${prefix}.${extension}.csi"),    emit: csi,  optional: true
     tuple val(meta), path("${prefix}.${extension}.bai"),    emit: bai,  optional: true
-    path  "versions.yml",                                   emit: versions
-
+    tuple val("${task.process}"), val('samtools'), eval("samtools version 2>&1 | tail -1"), topic: versions, emit: versions_samtools
+    
     when:
     task.ext.when == null || task.ext.when
 
@@ -53,10 +53,6 @@ process SAMTOOLS_SORT {
         -o ${output_file} \\
         -
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -77,10 +73,6 @@ process SAMTOOLS_SORT {
     """
     touch ${prefix}.${extension}
     ${index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+    
     """
 }
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 4c4010bbb36d..d873fd81e2d5 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -110,13 +110,27 @@ output:
           description: BAM index file (optional)
           pattern: "*.bai"
           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: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - samtools version 2>&1 | tail -1:
+          type: string
+          description: The command used to generate the version of the tool
+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"
   - "@ewels"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
index fa2778722f53..a5e779d98e6b 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -31,11 +31,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                        process.out.bam,
-                        process.out.bai,
-                        process.out.versions
-                ).match()}
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -63,11 +59,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                        process.out.bam,
-                        process.out.bai,
-                        process.out.versions
-                ).match()}
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -98,7 +90,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi,
-                        process.out.versions
+                        process.out.versions_samtools
                 ).match()}
             )
         }
@@ -133,7 +125,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.versions_samtools
                 ).match()}
             )
         }
@@ -168,7 +160,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.versions_samtools
                 ).match()}
             )
         }
@@ -203,7 +195,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.versions_samtools
                 ).match()}
             )
         }
@@ -235,7 +227,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } },
                     process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.versions
+                    process.out.versions_samtools
                 ).match()}
             )
         }
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index 473e17450357..2333cb9c5c99 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -20,14 +20,52 @@
                 ]
             ],
             [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                [
+                    "SAMTOOLS_SORT",
+                    "samtools",
+                    "    mem:\t mem"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:31.395604"
+        "timestamp": "2025-10-28T15:09:51.778909"
+    },
+    "bam_csi_index": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,72ca1dff5344a5e5e6b892fe5f6b134d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8"
+                ]
+            ],
+            [
+                [
+                    "SAMTOOLS_SORT",
+                    "samtools",
+                    "    mem:\t mem"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:09:23.735422"
     },
     "bam - stub": {
         "content": [
@@ -57,7 +95,11 @@
                     
                 ],
                 "6": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ],
                 "bai": [
                     
@@ -83,46 +125,20 @@
                 "sam": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:43:37.387063"
-    },
-    "bam_csi_index": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam:md5,72ca1dff5344a5e5e6b892fe5f6b134d"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8"
-                ]
-            ],
-            [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:06.976036"
+        "timestamp": "2025-10-28T15:09:56.812225"
     },
     "multiple bam bai index": {
         "content": [
@@ -145,14 +161,18 @@
                 ]
             ],
             [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                [
+                    "SAMTOOLS_SORT",
+                    "samtools",
+                    "    mem:\t mem"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:18.72271"
+        "timestamp": "2025-10-28T15:09:37.987389"
     },
     "cram - stub": {
         "content": [
@@ -182,7 +202,11 @@
                     
                 ],
                 "6": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ],
                 "bai": [
                     
@@ -208,16 +232,20 @@
                 "sam": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:48.734367"
+        "timestamp": "2025-10-28T15:10:07.407051"
     },
     "multiple bam": {
         "content": [
@@ -234,14 +262,18 @@
                 
             ],
             [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                [
+                    "SAMTOOLS_SORT",
+                    "samtools",
+                    "    mem:\t mem"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:12.989244"
+        "timestamp": "2025-10-28T15:09:29.814582"
     },
     "multiple bam - stub": {
         "content": [
@@ -271,7 +303,11 @@
                     
                 ],
                 "6": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ],
                 "bai": [
                     
@@ -297,40 +333,93 @@
                 "sam": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:43.196638"
+        "timestamp": "2025-10-28T15:10:02.429944"
     },
     "bam_no_index": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
+                ],
+                "bai": [
+                    
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:42:54.926504"
+        "timestamp": "2025-10-28T15:09:13.096776"
     },
     "multiple bam csi index": {
         "content": [
@@ -352,74 +441,103 @@
                     "test.sorted.bam.csi"
                 ]
             ],
-            [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-10T14:43:25.059178"
-    },
-    "bam": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc"
-                ]
-            ],
             [
                 [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam.csi"
+                    "SAMTOOLS_SORT",
+                    "samtools",
+                    "    mem:\t mem"
                 ]
-            ],
-            [
-                "versions.yml:md5,2659b187d681241451539d4c53500b9f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.09.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-10-08T11:59:46.372244"
+        "timestamp": "2025-10-28T15:09:46.029137"
     },
     "bam_bai_index": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
+                    ]
+                ],
+                "6": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "cram": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "sam": [
+                    
+                ],
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "    mem:\t mem"
+                    ]
                 ]
-            ],
-            [
-                "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2"
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T14:43:00.82974"
+        "timestamp": "2025-10-28T15:09:18.053161"
     }
 }
\ No newline at end of file

From 08b46dbbd55af9dd3efe0adee8cd1ac427c0fce1 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 16:30:00 +0100
Subject: [PATCH 02/10] feat: update samtools sort module with version topic
 support

---
 modules/nf-core/samtools/sort/meta.yml | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index d873fd81e2d5..7f33a7cb74c0 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -49,7 +49,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.bam":
+      - ${prefix}.bam:
           type: file
           description: Sorted BAM file
           pattern: "*.{bam}"
@@ -60,7 +60,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.cram":
+      - ${prefix}.cram:
           type: file
           description: Sorted CRAM file
           pattern: "*.{cram}"
@@ -71,19 +71,18 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.sam":
+      - ${prefix}.sam:
           type: file
           description: Sorted SAM file
           pattern: "*.{sam}"
           ontologies: []
-
   crai:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.${extension}.crai":
+      - ${prefix}.${extension}.crai:
           type: file
           description: CRAM index file (optional)
           pattern: "*.crai"
@@ -94,7 +93,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.${extension}.csi":
+      - ${prefix}.${extension}.csi:
           type: file
           description: BAM index file (optional)
           pattern: "*.csi"
@@ -105,7 +104,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.${extension}.bai":
+      - ${prefix}.${extension}.bai:
           type: file
           description: BAM index file (optional)
           pattern: "*.bai"
@@ -117,9 +116,6 @@ output:
       - samtools:
           type: string
           description: The tool name
-      - samtools version 2>&1 | tail -1:
-          type: string
-          description: The command used to generate the version of the tool
 topics:
   - versions:
       - - process:

From 30a9404939154b1ffa8796142e52dd6a0130cd83 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 16:43:46 +0100
Subject: [PATCH 03/10] feat: update samtools sort module with version topic
 support

---
 modules/nf-core/samtools/sort/meta.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 7f33a7cb74c0..076809bb6167 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -116,6 +116,9 @@ output:
       - samtools:
           type: string
           description: The tool name
+      - samtools version 2>&1 | tail -1:
+          type: string
+          description: The command used to generate the version of the tool
 topics:
   - versions:
       - - process:

From 02858fc6df9e02c53990063b6227a888128ba4fb Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 16:47:01 +0100
Subject: [PATCH 04/10] feat: update samtools sort module with version topic
 support

---
 .../samtools/sort/tests/main.nf.test.snap     |  20 +-
 modules/nf-core/shapeit5/phasecommon/meta.yml | 184 +++++++++---------
 2 files changed, 102 insertions(+), 102 deletions(-)

diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index 2333cb9c5c99..570e0a523018 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -31,7 +31,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:51.778909"
+        "timestamp": "2025-10-28T16:12:42.0061"
     },
     "bam_csi_index": {
         "content": [
@@ -65,7 +65,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:23.735422"
+        "timestamp": "2025-10-28T16:12:15.904021"
     },
     "bam - stub": {
         "content": [
@@ -138,7 +138,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:56.812225"
+        "timestamp": "2025-10-28T16:12:51.260116"
     },
     "multiple bam bai index": {
         "content": [
@@ -172,7 +172,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:37.987389"
+        "timestamp": "2025-10-28T16:12:29.239081"
     },
     "cram - stub": {
         "content": [
@@ -245,7 +245,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:10:07.407051"
+        "timestamp": "2025-10-28T16:13:02.354961"
     },
     "multiple bam": {
         "content": [
@@ -273,7 +273,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:29.814582"
+        "timestamp": "2025-10-28T16:12:23.805511"
     },
     "multiple bam - stub": {
         "content": [
@@ -346,7 +346,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:10:02.429944"
+        "timestamp": "2025-10-28T16:12:57.335298"
     },
     "bam_no_index": {
         "content": [
@@ -419,7 +419,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:13.096776"
+        "timestamp": "2025-10-28T16:12:03.756397"
     },
     "multiple bam csi index": {
         "content": [
@@ -453,7 +453,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:46.029137"
+        "timestamp": "2025-10-28T16:12:34.918284"
     },
     "bam_bai_index": {
         "content": [
@@ -538,6 +538,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:09:18.053161"
+        "timestamp": "2025-10-28T16:12:09.190395"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shapeit5/phasecommon/meta.yml b/modules/nf-core/shapeit5/phasecommon/meta.yml
index b88722bfa694..6ce521ecd955 100644
--- a/modules/nf-core/shapeit5/phasecommon/meta.yml
+++ b/modules/nf-core/shapeit5/phasecommon/meta.yml
@@ -2,108 +2,108 @@ name: "shapeit5_phasecommon"
 description: Tool to phase common sites, typically SNP array data, or the first step
   of WES/WGS data.
 keywords:
-  - phasing
-  - haplotype
-  - shapeit
+- phasing
+- haplotype
+- shapeit
 tools:
-  - "shapeit5":
-      description: "Fast and accurate method for estimation of haplotypes (phasing)"
-      homepage: "https://odelaneau.github.io/shapeit5/"
-      documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
-      tool_dev_url: "https://github.com/odelaneau/shapeit5"
-      doi: "10.1101/2022.10.19.512867 "
-      licence: ["MIT"]
-      identifier: biotools:shapeit5
+- "shapeit5":
+    description: "Fast and accurate method for estimation of haplotypes (phasing)"
+    homepage: "https://odelaneau.github.io/shapeit5/"
+    documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
+    tool_dev_url: "https://github.com/odelaneau/shapeit5"
+    doi: "10.1101/2022.10.19.512867 "
+    licence: ["MIT"]
+    identifier: biotools:shapeit5
 input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: |
+        Target dataset in VCF/BCF format defined at all variable positions.
+        The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
+      pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+      ontologies: []
+  - input_index:
+      type: file
+      description: Index file of the input VCF/BCF file containing genotype likelihoods.
+      pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
+      ontologies: []
+  - pedigree:
+      type: file
+      description: |
+        Pedigree information in the following format: offspring father mother.
+      pattern: "*.{txt, tsv}"
+      ontologies: []
+  - region:
+      type: string
+      description: |
+        Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
+        For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
+      pattern: "chrXX:leftBufferPosition-rightBufferPosition"
+- - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reference:
+      type: file
+      description: Reference panel of haplotypes in VCF/BCF format.
+      pattern: "*.{vcf.gz,bcf.gz}"
+      ontologies: []
+  - reference_index:
+      type: file
+      description: Index file of the Reference panel file.
+      pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
+      ontologies: []
+- - meta3:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - scaffold:
+      type: file
+      description: Scaffold of haplotypes in VCF/BCF format.
+      pattern: "*.{vcf.gz,bcf.gz}"
+      ontologies: []
+  - scaffold_index:
+      type: file
+      description: Index file of the scaffold file.
+      pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
+      ontologies: []
+- - meta4:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - map:
+      type: file
+      description: File containing the genetic map.
+      pattern: "*.gmap"
+      ontologies: []
+output:
+  phased_variant:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - input:
+    - "*.{vcf,bcf,vcf.gz,bcf.gz}":
         type: file
-        description: |
-          Target dataset in VCF/BCF format defined at all variable positions.
-          The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
+        description: Phased variant dataset in VCF/BCF format.
         pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
         ontologies: []
-    - input_index:
-        type: file
-        description: Index file of the input VCF/BCF file containing genotype likelihoods.
-        pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-        ontologies: []
-    - pedigree:
-        type: file
-        description: |
-          Pedigree information in the following format: offspring father mother.
-        pattern: "*.{txt, tsv}"
-        ontologies: []
-    - region:
-        type: string
-        description: |
-          Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
-          For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
-        pattern: "chrXX:leftBufferPosition-rightBufferPosition"
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - reference:
-        type: file
-        description: Reference panel of haplotypes in VCF/BCF format.
-        pattern: "*.{vcf.gz,bcf.gz}"
-        ontologies: []
-    - reference_index:
-        type: file
-        description: Index file of the Reference panel file.
-        pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-        ontologies: []
-  - - meta3:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - scaffold:
-        type: file
-        description: Scaffold of haplotypes in VCF/BCF format.
-        pattern: "*.{vcf.gz,bcf.gz}"
-        ontologies: []
-    - scaffold_index:
-        type: file
-        description: Index file of the scaffold file.
-        pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-        ontologies: []
-  - - meta4:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - map:
-        type: file
-        description: File containing the genetic map.
-        pattern: "*.gmap"
-        ontologies: []
-output:
-  phased_variant:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.{vcf,bcf,vcf.gz,bcf.gz}":
-          type: file
-          description: Phased variant dataset in VCF/BCF format.
-          pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-          ontologies: []
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+      ontologies:
+      - edam: http://edamontology.org/format_3750     # YAML
 authors:
-  - "@LouisLeNezet"
+- "@LouisLeNezet"
 maintainers:
-  - "@LouisLeNezet"
+- "@LouisLeNezet"

From 777b6da4a40e4193b7d26813f334b0eff1d94882 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 17:16:09 +0100
Subject: [PATCH 05/10] feat: update samtools sort module with version topic
 support

---
 .../samtools/sort/tests/main.nf.test.snap     | 50 +++++++++----------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index 570e0a523018..c9e2a40239a6 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -23,7 +23,7 @@
                 [
                     "SAMTOOLS_SORT",
                     "samtools",
-                    "    mem:\t mem"
+                    "1.22.1"
                 ]
             ]
         ],
@@ -31,7 +31,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:42.0061"
+        "timestamp": "2025-10-28T17:14:02.017643"
     },
     "bam_csi_index": {
         "content": [
@@ -57,7 +57,7 @@
                 [
                     "SAMTOOLS_SORT",
                     "samtools",
-                    "    mem:\t mem"
+                    "1.22.1"
                 ]
             ]
         ],
@@ -65,7 +65,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:15.904021"
+        "timestamp": "2025-10-28T17:13:41.541928"
     },
     "bam - stub": {
         "content": [
@@ -98,7 +98,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ],
                 "bai": [
@@ -129,7 +129,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ]
             }
@@ -138,7 +138,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:51.260116"
+        "timestamp": "2025-10-28T17:14:06.48563"
     },
     "multiple bam bai index": {
         "content": [
@@ -164,7 +164,7 @@
                 [
                     "SAMTOOLS_SORT",
                     "samtools",
-                    "    mem:\t mem"
+                    "1.22.1"
                 ]
             ]
         ],
@@ -172,7 +172,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:29.239081"
+        "timestamp": "2025-10-28T17:13:52.067223"
     },
     "cram - stub": {
         "content": [
@@ -205,7 +205,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ],
                 "bai": [
@@ -236,7 +236,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ]
             }
@@ -245,7 +245,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:13:02.354961"
+        "timestamp": "2025-10-28T17:14:16.941801"
     },
     "multiple bam": {
         "content": [
@@ -265,7 +265,7 @@
                 [
                     "SAMTOOLS_SORT",
                     "samtools",
-                    "    mem:\t mem"
+                    "1.22.1"
                 ]
             ]
         ],
@@ -273,7 +273,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:23.805511"
+        "timestamp": "2025-10-28T17:13:47.088129"
     },
     "multiple bam - stub": {
         "content": [
@@ -306,7 +306,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ],
                 "bai": [
@@ -337,7 +337,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ]
             }
@@ -346,7 +346,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:57.335298"
+        "timestamp": "2025-10-28T17:14:11.981828"
     },
     "bam_no_index": {
         "content": [
@@ -379,7 +379,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ],
                 "bai": [
@@ -410,7 +410,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ]
             }
@@ -419,7 +419,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:03.756397"
+        "timestamp": "2025-10-28T17:13:31.622188"
     },
     "multiple bam csi index": {
         "content": [
@@ -445,7 +445,7 @@
                 [
                     "SAMTOOLS_SORT",
                     "samtools",
-                    "    mem:\t mem"
+                    "1.22.1"
                 ]
             ]
         ],
@@ -453,7 +453,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:34.918284"
+        "timestamp": "2025-10-28T17:13:57.249125"
     },
     "bam_bai_index": {
         "content": [
@@ -492,7 +492,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ],
                 "bai": [
@@ -529,7 +529,7 @@
                     [
                         "SAMTOOLS_SORT",
                         "samtools",
-                        "    mem:\t mem"
+                        "1.22.1"
                     ]
                 ]
             }
@@ -538,6 +538,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:12:09.190395"
+        "timestamp": "2025-10-28T17:13:36.586805"
     }
 }
\ No newline at end of file

From 6c31c1c990bef9ca2c63ad895eb71071fa93d5a0 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Tue, 28 Oct 2025 17:28:57 +0100
Subject: [PATCH 06/10] feat: update samtools sort module with version topic
 support

---
 modules/nf-core/samtools/sort/main.nf  | 2 +-
 modules/nf-core/samtools/sort/meta.yml | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index d0b82510f34d..a12f6baab3c0 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -19,7 +19,7 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("${prefix}.${extension}.crai"),   emit: crai, optional: true
     tuple val(meta), path("${prefix}.${extension}.csi"),    emit: csi,  optional: true
     tuple val(meta), path("${prefix}.${extension}.bai"),    emit: bai,  optional: true
-    tuple val("${task.process}"), val('samtools'), eval("samtools version 2>&1 | tail -1"), topic: versions, emit: versions_samtools
+    tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -1 | sed 's/^.*samtools //'"), topic: versions, emit: versions_samtools
     
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 076809bb6167..7f33a7cb74c0 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -116,9 +116,6 @@ output:
       - samtools:
           type: string
           description: The tool name
-      - samtools version 2>&1 | tail -1:
-          type: string
-          description: The command used to generate the version of the tool
 topics:
   - versions:
       - - process:

From a4db227e6b58b55d257c74621472f38ffafa147c Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Wed, 29 Oct 2025 10:43:36 +0100
Subject: [PATCH 07/10] feat: update samtools sort module with version topic
 support

---
 modules/nf-core/samtools/sort/main.nf         |   2 +-
 modules/nf-core/samtools/sort/meta.yml        |   4 +
 .../nf-core/samtools/sort/tests/main.nf.test  |  28 +-
 .../samtools/sort/tests/main.nf.test.snap     | 407 ++++--------------
 4 files changed, 103 insertions(+), 338 deletions(-)

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index a12f6baab3c0..01e854bf77d1 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -19,7 +19,7 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("${prefix}.${extension}.crai"),   emit: crai, optional: true
     tuple val(meta), path("${prefix}.${extension}.csi"),    emit: csi,  optional: true
     tuple val(meta), path("${prefix}.${extension}.bai"),    emit: bai,  optional: true
-    tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | head -1 | sed 's/^.*samtools //'"), topic: versions, emit: versions_samtools
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
     
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 7f33a7cb74c0..349efebf4747 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -116,6 +116,10 @@ output:
       - samtools:
           type: string
           description: The tool name
+      - samtools version | sed '1!d;s/.* //':
+          type: string
+          description: The command used to generate the version of the tool
+
 topics:
   - versions:
       - - process:
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
index a5e779d98e6b..2696d74cc429 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test
@@ -31,7 +31,11 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.bai,
+                        process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match()}
             )
         }
     }
@@ -59,7 +63,11 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                        process.out.bam,
+                        process.out.bai,
+                        process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match()}
             )
         }
     }
@@ -90,7 +98,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi,
-                        process.out.versions_samtools
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -125,7 +133,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions_samtools
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -160,7 +168,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions_samtools
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -195,7 +203,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions_samtools
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -227,7 +235,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } },
                     process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.versions_samtools
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -257,7 +265,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
@@ -288,7 +296,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
@@ -317,7 +325,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index c9e2a40239a6..90441a271029 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -19,19 +19,21 @@
                     "test.sorted.cram.crai"
                 ]
             ],
-            [
-                [
-                    "SAMTOOLS_SORT",
-                    "samtools",
-                    "1.22.1"
+            {
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:14:02.017643"
+        "timestamp": "2025-10-29T10:39:35.989453"
     },
     "bam_csi_index": {
         "content": [
@@ -53,78 +55,25 @@
                     "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8"
                 ]
             ],
-            [
-                [
-                    "SAMTOOLS_SORT",
-                    "samtools",
-                    "1.22.1"
+            {
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:41.541928"
+        "timestamp": "2025-10-29T10:39:11.794807"
     },
     "bam - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    [
-                        "SAMTOOLS_SORT",
-                        "samtools",
-                        "1.22.1"
-                    ]
-                ],
-                "bai": [
-                    
-                ],
-                "bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "sam": [
-                    
-                ],
                 "versions_samtools": [
                     [
                         "SAMTOOLS_SORT",
@@ -138,7 +87,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:14:06.48563"
+        "timestamp": "2025-10-29T10:39:42.98507"
     },
     "multiple bam bai index": {
         "content": [
@@ -160,78 +109,25 @@
                     "test.sorted.bam.bai"
                 ]
             ],
-            [
-                [
-                    "SAMTOOLS_SORT",
-                    "samtools",
-                    "1.22.1"
+            {
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:52.067223"
+        "timestamp": "2025-10-29T10:39:24.37963"
     },
     "cram - stub": {
         "content": [
             {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    [
-                        "SAMTOOLS_SORT",
-                        "samtools",
-                        "1.22.1"
-                    ]
-                ],
-                "bai": [
-                    
-                ],
-                "bam": [
-                    
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "csi": [
-                    
-                ],
-                "sam": [
-                    
-                ],
                 "versions_samtools": [
                     [
                         "SAMTOOLS_SORT",
@@ -245,7 +141,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:14:16.941801"
+        "timestamp": "2025-10-29T10:39:56.969304"
     },
     "multiple bam": {
         "content": [
@@ -261,78 +157,25 @@
             [
                 
             ],
-            [
-                [
-                    "SAMTOOLS_SORT",
-                    "samtools",
-                    "1.22.1"
+            {
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:47.088129"
+        "timestamp": "2025-10-29T10:39:18.450196"
     },
     "multiple bam - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    [
-                        "SAMTOOLS_SORT",
-                        "samtools",
-                        "1.22.1"
-                    ]
-                ],
-                "bai": [
-                    
-                ],
-                "bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "sam": [
-                    
-                ],
                 "versions_samtools": [
                     [
                         "SAMTOOLS_SORT",
@@ -346,66 +189,23 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:14:11.981828"
+        "timestamp": "2025-10-29T10:39:50.404875"
     },
     "bam_no_index": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
+                ]
+            ],
+            [
+                
+            ],
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    [
-                        "SAMTOOLS_SORT",
-                        "samtools",
-                        "1.22.1"
-                    ]
-                ],
-                "bai": [
-                    
-                ],
-                "bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "sam": [
-                    
-                ],
                 "versions_samtools": [
                     [
                         "SAMTOOLS_SORT",
@@ -419,7 +219,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:31.622188"
+        "timestamp": "2025-10-29T10:39:02.047578"
     },
     "multiple bam csi index": {
         "content": [
@@ -441,90 +241,43 @@
                     "test.sorted.bam.csi"
                 ]
             ],
-            [
-                [
-                    "SAMTOOLS_SORT",
-                    "samtools",
-                    "1.22.1"
+            {
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_SORT",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:57.249125"
+        "timestamp": "2025-10-29T10:39:30.511113"
     },
     "bam_bai_index": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
+                ]
+            ],
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
-                    ]
-                ],
-                "6": [
-                    [
-                        "SAMTOOLS_SORT",
-                        "samtools",
-                        "1.22.1"
-                    ]
-                ],
-                "bai": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0"
-                    ]
-                ],
-                "bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54"
-                    ]
-                ],
-                "crai": [
-                    
-                ],
-                "cram": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "sam": [
-                    
-                ],
                 "versions_samtools": [
                     [
                         "SAMTOOLS_SORT",
@@ -538,6 +291,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T17:13:36.586805"
+        "timestamp": "2025-10-29T10:39:06.97914"
     }
 }
\ No newline at end of file

From 046b95bec6dacecfecea2612b49d6e7369633ef2 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Wed, 29 Oct 2025 12:50:10 +0100
Subject: [PATCH 08/10] Update meta.yml and test snapshot

---
 modules/nf-core/samtools/sort/meta.yml        | 12 +++++------
 .../samtools/sort/tests/main.nf.test.snap     | 20 +++++++++----------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
index 349efebf4747..08a6627501d4 100644
--- a/modules/nf-core/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -49,7 +49,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.bam:
+      - "${prefix}.bam":
           type: file
           description: Sorted BAM file
           pattern: "*.{bam}"
@@ -60,7 +60,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.cram:
+      - "${prefix}.cram":
           type: file
           description: Sorted CRAM file
           pattern: "*.{cram}"
@@ -71,7 +71,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.sam:
+      - "${prefix}.sam":
           type: file
           description: Sorted SAM file
           pattern: "*.{sam}"
@@ -82,7 +82,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.${extension}.crai:
+      - "${prefix}.${extension}.crai":
           type: file
           description: CRAM index file (optional)
           pattern: "*.crai"
@@ -93,7 +93,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.${extension}.csi:
+      - "${prefix}.${extension}.csi":
           type: file
           description: BAM index file (optional)
           pattern: "*.csi"
@@ -104,7 +104,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.${extension}.bai:
+      - "${prefix}.${extension}.bai":
           type: file
           description: BAM index file (optional)
           pattern: "*.bai"
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
index 90441a271029..4e618fa3f810 100644
--- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
@@ -33,7 +33,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:35.989453"
+        "timestamp": "2025-10-29T12:47:01.171084"
     },
     "bam_csi_index": {
         "content": [
@@ -69,7 +69,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:11.794807"
+        "timestamp": "2025-10-29T12:46:00.961675"
     },
     "bam - stub": {
         "content": [
@@ -87,7 +87,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:42.98507"
+        "timestamp": "2025-10-29T12:47:12.154354"
     },
     "multiple bam bai index": {
         "content": [
@@ -123,7 +123,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:24.37963"
+        "timestamp": "2025-10-29T12:46:25.488622"
     },
     "cram - stub": {
         "content": [
@@ -141,7 +141,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:56.969304"
+        "timestamp": "2025-10-29T12:47:28.485045"
     },
     "multiple bam": {
         "content": [
@@ -171,7 +171,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:18.450196"
+        "timestamp": "2025-10-29T12:46:13.168476"
     },
     "multiple bam - stub": {
         "content": [
@@ -189,7 +189,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:50.404875"
+        "timestamp": "2025-10-29T12:47:21.628088"
     },
     "bam_no_index": {
         "content": [
@@ -219,7 +219,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:02.047578"
+        "timestamp": "2025-10-29T12:45:47.139418"
     },
     "multiple bam csi index": {
         "content": [
@@ -255,7 +255,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:30.511113"
+        "timestamp": "2025-10-29T12:46:51.5531"
     },
     "bam_bai_index": {
         "content": [
@@ -291,6 +291,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T10:39:06.97914"
+        "timestamp": "2025-10-29T12:45:52.796936"
     }
 }
\ No newline at end of file

From a97a7a2bccd5a67a5e8b629054759265bd304945 Mon Sep 17 00:00:00 2001
From: wangdepin <wangdepin5135@gmail.com>
Date: Wed, 29 Oct 2025 15:31:15 +0100
Subject: [PATCH 09/10] remove .devcontainer

---
 .devcontainer/devcontainer.json | 20 --------------------
 .devcontainer/setup.sh          | 15 ---------------
 2 files changed, 35 deletions(-)
 delete mode 100644 .devcontainer/devcontainer.json
 delete mode 100755 .devcontainer/setup.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
deleted file mode 100644
index bfd2674810ff..000000000000
--- a/.devcontainer/devcontainer.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
-    "name": "nfcore-modules",
-    "image": "nfcore/devcontainer:dev",
-
-    "remoteEnv": {
-        // Workspace path on the host for mounting with docker-outside-of-docker
-        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
-    },
-
-    "onCreateCommand": "./.devcontainer/setup.sh",
-
-    "remoteUser": "root",
-    "privileged": true,
-
-    "hostRequirements": {
-        "cpus": 4,
-        "memory": "16gb",
-        "storage": "32gb"
-    }
-}
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
deleted file mode 100755
index 5269d8566074..000000000000
--- a/.devcontainer/setup.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env bash
-
-# Customise the terminal command prompt
-echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
-echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
-export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
-
-# Update Nextflow
-nextflow self-update
-
-# Install pre-commit hooks
-pre-commit install --install-hooks
-
-# Update welcome message
-echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 8bc50559a052e9e8cda6ab5860db4d3a027191dc Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <marcel@seqera.io>
Date: Wed, 29 Oct 2025 16:44:39 +0100
Subject: [PATCH 10/10] Revert "remove .devcontainer"

This reverts commit a97a7a2bccd5a67a5e8b629054759265bd304945.
---
 .devcontainer/devcontainer.json | 20 ++++++++++++++++++++
 .devcontainer/setup.sh          | 15 +++++++++++++++
 2 files changed, 35 insertions(+)
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100755 .devcontainer/setup.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 000000000000..bfd2674810ff
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,20 @@
+{
+    "name": "nfcore-modules",
+    "image": "nfcore/devcontainer:dev",
+
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "remoteUser": "root",
+    "privileged": true,
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
+    }
+}
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 000000000000..5269d8566074
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Install pre-commit hooks
+pre-commit install --install-hooks
+
+# Update welcome message
+echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt