Update pairtools to 1.1.3 and migrating to topic version

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

modules/nf-core/pairtools/dedup/main.nf

@@ -2,20 +2,18 @@ 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)
 
     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
     """
 }

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:

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()
 				}
             )

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"
+        }
     }
 }

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

modules/nf-core/pairtools/flip/main.nf

@@ -2,20 +2,18 @@ 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)
     path chromsizes
 
     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
     """
 }

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:

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()
 				}
             )

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"
+        }
     }
 }

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

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
     """
 }

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:

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()
 				}
             )

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"
+        }
     }
 }

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