diff --git a/modules/nf-core/pairtools/dedup/environment.yml b/modules/nf-core/pairtools/dedup/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/dedup/environment.yml
+++ b/modules/nf-core/pairtools/dedup/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/dedup/main.nf b/modules/nf-core/pairtools/dedup/main.nf
index b5a3f7559369..51bf052614f3 100644
--- a/modules/nf-core/pairtools/dedup/main.nf
+++ b/modules/nf-core/pairtools/dedup/main.nf
@@ -2,12 +2,10 @@ process PAIRTOOLS_DEDUP {
     tag "$meta.id"
     label 'process_high'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(input)
@@ -15,7 +13,7 @@ process PAIRTOOLS_DEDUP {
     output:
     tuple val(meta), path("*.pairs.gz")  , emit: pairs
     tuple val(meta), path("*.pairs.stat"), emit: stat
-    path "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,10 +27,5 @@ process PAIRTOOLS_DEDUP {
         -o ${prefix}.pairs.gz \\
         --output-stats ${prefix}.pairs.stat \\
         $input
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/dedup/meta.yml b/modules/nf-core/pairtools/dedup/meta.yml
index 039102061e06..4b7495366efd 100644
--- a/modules/nf-core/pairtools/dedup/meta.yml
+++ b/modules/nf-core/pairtools/dedup/meta.yml
@@ -11,7 +11,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -46,13 +47,27 @@ output:
           description: stats of the pairs
           pattern: "*.{pairs.stat}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
 maintainers:
diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test b/modules/nf-core/pairtools/dedup/tests/main.nf.test
index c812a6ac211d..0058efbe13f8 100644
--- a/modules/nf-core/pairtools/dedup/tests/main.nf.test
+++ b/modules/nf-core/pairtools/dedup/tests/main.nf.test
@@ -29,7 +29,7 @@ nextflow_process {
                 { assert snapshot(
 					path(process.out.pairs[0][1]).linesGzip[3..7],
 					process.out.stat,
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap b/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
index 46dcf9654b70..5ab5863a3061 100644
--- a/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
@@ -14,17 +14,23 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.dedup.pairs.stat:md5,94682d1bc608ade150dd11993fbfd2a3"
+                    "test.dedup.pairs.stat:md5,d31a54a0a28e2687c6ece6ddf970dd5a"
                 ]
             ],
-            [
-                "versions.yml:md5,485fbdd68f35d563c8559e1afedc4c53"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_DEDUP",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:32:18.794533874",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:23:16.451408"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/flip/environment.yml b/modules/nf-core/pairtools/flip/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/flip/environment.yml
+++ b/modules/nf-core/pairtools/flip/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/flip/main.nf b/modules/nf-core/pairtools/flip/main.nf
index e41d0bc87414..1a7f656d7594 100644
--- a/modules/nf-core/pairtools/flip/main.nf
+++ b/modules/nf-core/pairtools/flip/main.nf
@@ -2,12 +2,10 @@ process PAIRTOOLS_FLIP {
     tag "$meta.id"
     label 'process_low'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(sam)
@@ -15,7 +13,7 @@ process PAIRTOOLS_FLIP {
 
     output:
     tuple val(meta), path("*.flip.gz"), emit: flip
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,10 +28,5 @@ process PAIRTOOLS_FLIP {
         $args \\
         -o ${prefix}.flip.gz \\
         $sam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/flip/meta.yml b/modules/nf-core/pairtools/flip/meta.yml
index b23b81b578f3..59c7ef65f0c2 100644
--- a/modules/nf-core/pairtools/flip/meta.yml
+++ b/modules/nf-core/pairtools/flip/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -38,13 +39,27 @@ output:
           description: output file of flip
           pattern: "*.{flip.gz}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
 maintainers:
diff --git a/modules/nf-core/pairtools/flip/tests/main.nf.test b/modules/nf-core/pairtools/flip/tests/main.nf.test
index 9d507bc84e47..d845e8934197 100644
--- a/modules/nf-core/pairtools/flip/tests/main.nf.test
+++ b/modules/nf-core/pairtools/flip/tests/main.nf.test
@@ -28,7 +28,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.flip[0][1]).linesGzip[3..7],
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/flip/tests/main.nf.test.snap b/modules/nf-core/pairtools/flip/tests/main.nf.test.snap
index 06deeae99411..c04fd6ca640d 100644
--- a/modules/nf-core/pairtools/flip/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/flip/tests/main.nf.test.snap
@@ -8,14 +8,20 @@
                 "#samheader: @SQ\tSN:chr1\tLN:10000",
                 "#samheader: @SQ\tSN:chr2\tLN:10000"
             ],
-            [
-                "versions.yml:md5,1152374357606db444ce2a2cdb340080"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_FLIP",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:56:20.591962751",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:21:02.024673"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/merge/environment.yml b/modules/nf-core/pairtools/merge/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/merge/environment.yml
+++ b/modules/nf-core/pairtools/merge/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/merge/main.nf b/modules/nf-core/pairtools/merge/main.nf
index 4893347783b9..ca04d193d7a9 100644
--- a/modules/nf-core/pairtools/merge/main.nf
+++ b/modules/nf-core/pairtools/merge/main.nf
@@ -1,20 +1,18 @@
 process PAIRTOOLS_MERGE {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_medium'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(allpairs)
 
     output:
     tuple val(meta), path("*pairs.gz"), emit:pairs
-    path("versions.yml"), emit:versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,10 +26,5 @@ process PAIRTOOLS_MERGE {
         --nproc ${task.cpus} \
         -o ${prefix}.pairs.gz \
         ${allpairs}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/merge/meta.yml b/modules/nf-core/pairtools/merge/meta.yml
index d76b0923f840..260cad606b40 100644
--- a/modules/nf-core/pairtools/merge/meta.yml
+++ b/modules/nf-core/pairtools/merge/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -34,13 +35,27 @@ output:
           description: Merged pairs file
           pattern: "*.{pairs.gz}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nservant"
 maintainers:
diff --git a/modules/nf-core/pairtools/merge/tests/main.nf.test b/modules/nf-core/pairtools/merge/tests/main.nf.test
index 8d2b9d8dfcba..dd7f276db22b 100644
--- a/modules/nf-core/pairtools/merge/tests/main.nf.test
+++ b/modules/nf-core/pairtools/merge/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.pairs[0][1]).linesGzip[3..7],
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/merge/tests/main.nf.test.snap b/modules/nf-core/pairtools/merge/tests/main.nf.test.snap
index 3aabbca339d3..42985a3d1c28 100644
--- a/modules/nf-core/pairtools/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/merge/tests/main.nf.test.snap
@@ -8,14 +8,20 @@
                 "#samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -SP /path/ucsc.hg19.fasta.gz /path/1.fastq.gz /path/2.fastq.gz",
                 "#chromosomes: chr2 chr3 chr1"
             ],
-            [
-                "versions.yml:md5,e0acb3bd173f64f9984f597571e80eb0"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_MERGE",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:56:36.065456442",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:19:28.360208"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/parse/environment.yml b/modules/nf-core/pairtools/parse/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/parse/environment.yml
+++ b/modules/nf-core/pairtools/parse/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/parse/main.nf b/modules/nf-core/pairtools/parse/main.nf
index b9394925c47e..195fc7dde75e 100644
--- a/modules/nf-core/pairtools/parse/main.nf
+++ b/modules/nf-core/pairtools/parse/main.nf
@@ -2,12 +2,10 @@ process PAIRTOOLS_PARSE {
     tag "$meta.id"
     label 'process_low'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -16,7 +14,7 @@ process PAIRTOOLS_PARSE {
     output:
     tuple val(meta), path("*.pairsam.gz")  , emit: pairsam
     tuple val(meta), path("*.pairsam.stat"), emit: stat
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,10 +30,5 @@ process PAIRTOOLS_PARSE {
         --output-stats ${prefix}.pairsam.stat \\
         -o ${prefix}.pairsam.gz \\
         $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/parse/meta.yml b/modules/nf-core/pairtools/parse/meta.yml
index 2438df7aec3b..f396e697e0a2 100644
--- a/modules/nf-core/pairtools/parse/meta.yml
+++ b/modules/nf-core/pairtools/parse/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -50,13 +51,27 @@ output:
           description: stats of the pairs
           pattern: "*.{pairsam.stat}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
 maintainers:
diff --git a/modules/nf-core/pairtools/parse/tests/main.nf.test b/modules/nf-core/pairtools/parse/tests/main.nf.test
index 0535d4dde825..287f2e04b6f5 100644
--- a/modules/nf-core/pairtools/parse/tests/main.nf.test
+++ b/modules/nf-core/pairtools/parse/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert snapshot(
 					path(process.out.pairsam[0][1]).linesGzip[3..7],
 					process.out.stat,
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/parse/tests/main.nf.test.snap b/modules/nf-core/pairtools/parse/tests/main.nf.test.snap
index c06e572cd5fd..a2f44cd0dc03 100644
--- a/modules/nf-core/pairtools/parse/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/parse/tests/main.nf.test.snap
@@ -14,17 +14,23 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.raw.pairsam.stat:md5,054bf78ee4f0a4c447ad3eeb81f1f4ae"
+                    "test.raw.pairsam.stat:md5,bdca4672c0f0325d6882b8417651334b"
                 ]
             ],
-            [
-                "versions.yml:md5,2c8cb00722749f8e3831464a5057c519"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_PARSE",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:56:51.564599797",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:17:35.185642"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/restrict/environment.yml b/modules/nf-core/pairtools/restrict/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/restrict/environment.yml
+++ b/modules/nf-core/pairtools/restrict/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/restrict/main.nf b/modules/nf-core/pairtools/restrict/main.nf
index dd57cebdc8f6..843608fbc50e 100644
--- a/modules/nf-core/pairtools/restrict/main.nf
+++ b/modules/nf-core/pairtools/restrict/main.nf
@@ -2,12 +2,10 @@ process PAIRTOOLS_RESTRICT {
     tag "$meta.id"
     label 'process_high'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(pairs)
@@ -15,7 +13,7 @@ process PAIRTOOLS_RESTRICT {
 
     output:
     tuple val(meta), path("*.pairs.gz"), emit: restrict
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,10 +28,5 @@ process PAIRTOOLS_RESTRICT {
         $args \\
         -o ${prefix}.pairs.gz \\
         $pairs
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/restrict/meta.yml b/modules/nf-core/pairtools/restrict/meta.yml
index 126aeee7a0a2..164e0fec86f6 100644
--- a/modules/nf-core/pairtools/restrict/meta.yml
+++ b/modules/nf-core/pairtools/restrict/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -41,13 +42,27 @@ output:
           description: Filtered pairs file
           pattern: "*.{pairs.gz}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
 maintainers:
diff --git a/modules/nf-core/pairtools/restrict/tests/main.nf.test b/modules/nf-core/pairtools/restrict/tests/main.nf.test
index b9fa5c8723c2..d82055b5bc5b 100644
--- a/modules/nf-core/pairtools/restrict/tests/main.nf.test
+++ b/modules/nf-core/pairtools/restrict/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.restrict[0][1]).linesGzip[3..7],
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap b/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap
index b56cc90ce067..f637d8d9d338 100644
--- a/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/restrict/tests/main.nf.test.snap
@@ -8,14 +8,20 @@
                 "#samheader: @SQ\tSN:chr1\tLN:10000",
                 "#samheader: @SQ\tSN:chr2\tLN:10000"
             ],
-            [
-                "versions.yml:md5,c67dacbd4b0c4f2f060bd65b776113da"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_RESTRICT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:57:07.368536025",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:15:44.880469"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/select/environment.yml b/modules/nf-core/pairtools/select/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/select/environment.yml
+++ b/modules/nf-core/pairtools/select/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/select/main.nf b/modules/nf-core/pairtools/select/main.nf
index 69e8d47fdfda..4af58fa31db9 100644
--- a/modules/nf-core/pairtools/select/main.nf
+++ b/modules/nf-core/pairtools/select/main.nf
@@ -2,12 +2,10 @@ process PAIRTOOLS_SELECT {
     tag "$meta.id"
     label 'process_medium'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(input)
@@ -15,7 +13,7 @@ process PAIRTOOLS_SELECT {
     output:
     tuple val(meta), path("*.selected.pairs.gz")  , emit: selected
     tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected
-    path "versions.yml"                           , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,10 +27,5 @@ process PAIRTOOLS_SELECT {
         -o ${prefix}.selected.pairs.gz \\
         --output-rest ${prefix}.unselected.pairs.gz \\
         ${input}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/select/meta.yml b/modules/nf-core/pairtools/select/meta.yml
index cad52489d6c8..d21c3ba7c34d 100644
--- a/modules/nf-core/pairtools/select/meta.yml
+++ b/modules/nf-core/pairtools/select/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -45,13 +46,27 @@ output:
           description: Rest pairs file.
           pattern: "*.{unselected.pairs.gz}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
 maintainers:
diff --git a/modules/nf-core/pairtools/select/tests/main.nf.test b/modules/nf-core/pairtools/select/tests/main.nf.test
index de7833405dfc..d64b66c76096 100644
--- a/modules/nf-core/pairtools/select/tests/main.nf.test
+++ b/modules/nf-core/pairtools/select/tests/main.nf.test
@@ -29,7 +29,7 @@ nextflow_process {
                 { assert snapshot(
 					path(process.out.selected[0][1]).linesGzip[3..7],
 					path(process.out.unselected[0][1]).linesGzip[3..7],
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/select/tests/main.nf.test.snap b/modules/nf-core/pairtools/select/tests/main.nf.test.snap
index d4361209f78b..2dfede2946a4 100644
--- a/modules/nf-core/pairtools/select/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/select/tests/main.nf.test.snap
@@ -15,14 +15,20 @@
                 "#chromsize: chr1 100",
                 "#samheader: @SQ\tSN:chr1\tLN:100"
             ],
-            [
-                "versions.yml:md5,ca2f02d3bd0e277e9f578067ff87c19d"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_SELECT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:57:22.099470463",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:13:46.44029"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/sort/environment.yml b/modules/nf-core/pairtools/sort/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/sort/environment.yml
+++ b/modules/nf-core/pairtools/sort/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/sort/main.nf b/modules/nf-core/pairtools/sort/main.nf
index 653a8d3b4e54..339974d2a958 100644
--- a/modules/nf-core/pairtools/sort/main.nf
+++ b/modules/nf-core/pairtools/sort/main.nf
@@ -2,19 +2,17 @@ process PAIRTOOLS_SORT {
     tag "$meta.id"
     label 'process_high'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(input)
 
     output:
     tuple val(meta), path("*.pairs.gz"), emit: sorted
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,10 +29,5 @@ process PAIRTOOLS_SORT {
         --memory ${buffer}G \\
         -o ${prefix}.pairs.gz \\
         $input
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/sort/meta.yml b/modules/nf-core/pairtools/sort/meta.yml
index a8239d450ba8..193381784ac3 100644
--- a/modules/nf-core/pairtools/sort/meta.yml
+++ b/modules/nf-core/pairtools/sort/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -34,13 +35,27 @@ output:
           description: Sorted pairs file
           pattern: "*.{pairs.gz}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jianhong"
   - "@nservant"
diff --git a/modules/nf-core/pairtools/sort/tests/main.nf.test b/modules/nf-core/pairtools/sort/tests/main.nf.test
index 8413a2b1e2e0..dcd4681b8489 100644
--- a/modules/nf-core/pairtools/sort/tests/main.nf.test
+++ b/modules/nf-core/pairtools/sort/tests/main.nf.test
@@ -28,7 +28,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.sorted[0][1]).linesGzip[3..7],
-					process.out.versions
+					process.out.findAll { key, val -> key.startsWith('versions') }
 					).match()
 				}
             )
diff --git a/modules/nf-core/pairtools/sort/tests/main.nf.test.snap b/modules/nf-core/pairtools/sort/tests/main.nf.test.snap
index 1b22f32856f1..1af25d504212 100644
--- a/modules/nf-core/pairtools/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/sort/tests/main.nf.test.snap
@@ -8,14 +8,20 @@
                 "#chromsize: chr3 100",
                 "#chromsize: chr1 100"
             ],
-            [
-                "versions.yml:md5,6f5e6b4260ee11d35e306d2e085fb762"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_SORT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:57:37.696891982",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:12:01.451816"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/split/environment.yml b/modules/nf-core/pairtools/split/environment.yml
index 11d51852f690..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/split/environment.yml
+++ b/modules/nf-core/pairtools/split/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  ## Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-  ## Not an issue with the biocontainers because they were built prior to numpy 1.24
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/split/main.nf b/modules/nf-core/pairtools/split/main.nf
index 51d34f21b26a..0b6e6b8b83a2 100644
--- a/modules/nf-core/pairtools/split/main.nf
+++ b/modules/nf-core/pairtools/split/main.nf
@@ -1,11 +1,11 @@
 process PAIRTOOLS_SPLIT {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0'
-        : 'biocontainers/pairtools:1.0.2--py39h2a9f597_0'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(pairs)
@@ -13,7 +13,7 @@ process PAIRTOOLS_SPLIT {
     output:
     tuple val(meta), path("*.split.pairs.gz"), emit: pairs
     tuple val(meta), path("*.bam"), emit: bam, optional: true
-    path ("versions.yml"), emit: versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,11 +28,6 @@ process PAIRTOOLS_SPLIT {
         --output-pairs ${prefix}.split.pairs.gz \
         ${args} \
         ${pairs}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools, version //')
-    END_VERSIONS
     """
 
     stub:
@@ -40,10 +35,5 @@ process PAIRTOOLS_SPLIT {
     """
     export MPLCONFIGDIR=tmp
     echo "" | gzip > ${prefix}.split.pairs.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | sed 's/pairtools, version //')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/split/meta.yml b/modules/nf-core/pairtools/split/meta.yml
index 14ab58c42f46..c33a480ade9c 100644
--- a/modules/nf-core/pairtools/split/meta.yml
+++ b/modules/nf-core/pairtools/split/meta.yml
@@ -10,9 +10,9 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
-
 input:
   - - meta:
         type: map
@@ -46,12 +46,26 @@ output:
           description: Output BAM file
           pattern: "*.bam"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nservant"
diff --git a/modules/nf-core/pairtools/split/tests/main.nf.test b/modules/nf-core/pairtools/split/tests/main.nf.test
index ad050dec9842..7ba5b2b88ef6 100644
--- a/modules/nf-core/pairtools/split/tests/main.nf.test
+++ b/modules/nf-core/pairtools/split/tests/main.nf.test
@@ -24,7 +24,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() },
                 { assert process.out.pairs.get(0).get(1).endsWith("test.split.pairs.gz") }
             )
         }
diff --git a/modules/nf-core/pairtools/split/tests/main.nf.test.snap b/modules/nf-core/pairtools/split/tests/main.nf.test.snap
index 8ede40a3c9d1..9d13f2b9206f 100644
--- a/modules/nf-core/pairtools/split/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/split/tests/main.nf.test.snap
@@ -1,15 +1,21 @@
 {
     "mock_pairsam": {
         "content": [
-            [
-                "versions.yml:md5,0a4fa42a3bf8a568f64d3b3c9b9b7097"
-            ]
+            {
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_SPLIT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-25T00:57:53.252123981",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-03T09:11:53.240905583"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "mock_pairsam - stub": {
         "content": [
@@ -27,7 +33,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,0a4fa42a3bf8a568f64d3b3c9b9b7097"
+                    [
+                        "PAIRTOOLS_SPLIT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
                 ],
                 "bam": [
                     
@@ -41,15 +51,19 @@
                         "test.split.pairs.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0a4fa42a3bf8a568f64d3b3c9b9b7097"
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_SPLIT",
+                        "pairtools",
+                        "1.1.3"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-25T00:58:06.429274925",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-10T14:06:06.314038764"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/stats/environment.yml b/modules/nf-core/pairtools/stats/environment.yml
index d2523556961e..e479ddec3bda 100644
--- a/modules/nf-core/pairtools/stats/environment.yml
+++ b/modules/nf-core/pairtools/stats/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pairtools=1.0.2
-  - conda-forge::numpy=1.23
+  - bioconda::pairtools=1.1.3
diff --git a/modules/nf-core/pairtools/stats/main.nf b/modules/nf-core/pairtools/stats/main.nf
index b07d06109490..af012881f453 100644
--- a/modules/nf-core/pairtools/stats/main.nf
+++ b/modules/nf-core/pairtools/stats/main.nf
@@ -1,20 +1,18 @@
 process PAIRTOOLS_STATS {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_low'
 
-    // Pinning numpy to 1.23 until https://github.com/open2c/pairtools/issues/170 is resolved
-    // Not an issue with the biocontainers because they were built prior to numpy 1.24
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pairtools:1.0.2--py39h2a9f597_0' :
-        'biocontainers/pairtools:1.0.2--py39h2a9f597_0' }"
+        'https://depot.galaxyproject.org/singularity/pairtools:1.1.3--py39h7a39fba_0' :
+        'biocontainers/pairtools:1.1.3--py39h7a39fba_0' }"
 
     input:
     tuple val(meta), path(pairs)
 
     output:
     tuple val(meta), path("*.pairs.stat"), emit:stats
-    path("versions.yml"), emit:versions
+    tuple val("${task.process}"), val('pairtools'), eval("pairtools --version | sed 's/.*pairtools.*version //'") , emit: versions_pairtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,10 +26,5 @@ process PAIRTOOLS_STATS {
         --nproc-in ${task.cpus} --nproc-out ${task.cpus} \\
         -o ${prefix}.pairs.stat \\
         ${pairs}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pairtools/stats/meta.yml b/modules/nf-core/pairtools/stats/meta.yml
index 49171b95137d..fda0df6d85bf 100644
--- a/modules/nf-core/pairtools/stats/meta.yml
+++ b/modules/nf-core/pairtools/stats/meta.yml
@@ -10,7 +10,8 @@ tools:
       homepage: http://pairtools.readthedocs.io/
       documentation: http://pairtools.readthedocs.io/
       tool_dev_url: https://github.com/mirnylab/pairtools
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -34,13 +35,27 @@ output:
           description: Pairs statistics
           pattern: "*{.pairs.stat}"
           ontologies: []
+  versions_pairtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pairtools:
+          type: string
+          description: The name of the tool
+      - pairtools --version | sed 's/.*pairtools.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nservant"
 maintainers:
diff --git a/modules/nf-core/pairtools/stats/tests/main.nf.test.snap b/modules/nf-core/pairtools/stats/tests/main.nf.test.snap
index 929db4545e73..d66675337df2 100644
--- a/modules/nf-core/pairtools/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/pairtools/stats/tests/main.nf.test.snap
@@ -8,11 +8,15 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.pairs.stat:md5,77a1b2b0b146e00313435f4a707d2d0d"
+                        "test.pairs.stat:md5,1fa52eb3afe37de214b909a252ede06d"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,97ccf9babab2e888f52934164b9ef0d8"
+                    [
+                        "PAIRTOOLS_STATS",
+                        "pairtools",
+                        "1.1.3"
+                    ]
                 ],
                 "stats": [
                     [
@@ -20,18 +24,22 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.pairs.stat:md5,77a1b2b0b146e00313435f4a707d2d0d"
+                        "test.pairs.stat:md5,1fa52eb3afe37de214b909a252ede06d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,97ccf9babab2e888f52934164b9ef0d8"
+                "versions_pairtools": [
+                    [
+                        "PAIRTOOLS_STATS",
+                        "pairtools",
+                        "1.1.3"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-25T00:58:21.625592452",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-23T11:05:50.844045"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file