Cnvpytor/importreaddepth

modules/nf-core/cnvpytor/importreaddepth/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::cnvpytor=1.3.1
-  - conda-forge::numpy=1.24.3
+  - bioconda::cnvpytor=1.3.2
+  - conda-forge::make=4.4.1

modules/nf-core/cnvpytor/importreaddepth/main.nf

@@ -4,8 +4,8 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:1.3.1--pyhdfd78af_1':
-        'biocontainers/cnvpytor:1.3.1--pyhdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bbb6343edff4191cb1f445b2aac028d1f805ed5a7d50799513c82531bcfdede5/data':
+        'community.wave.seqera.io/library/cnvpytor_make:a8fdcebe82041114' }"
 
     input:
     tuple val(meta), path(input_file), path(index)
@@ -14,7 +14,11 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     output:
     tuple val(meta), path("*.pytor")	, emit: pytor
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('cnvpytor'), val('1.3.2'), emit: versions_cnvpytor, topic: versions
+    // cnvpytor version is hardcoded due to this error when calling cnvpytor --version
+    // > cnvpytor --version
+    // 2026-03-13 16:14:08,088 - cnvpytor - ERROR - Some reference genome resource files are missing.
+    // Run 'cnvpytor -download' as same user who has installed cnvpytor.
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,21 +33,11 @@ process CNVPYTOR_IMPORTREADDEPTH {
         -rd $input_file \\
         $args \\
         $reference
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cnvpytor: \$(cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.pytor
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cnvpytor: \$(cnvpytor --version | sed -n 's/.*CNVpytor \\(.*\\)/\\1/p')
-    END_VERSIONS
     """
 }

modules/nf-core/cnvpytor/importreaddepth/meta.yml

@@ -1,6 +1,6 @@
 name: cnvpytor_importreaddepth
-description: command line tool for CNV/CNA analysis. This step imports the read depth
-  data into a root pytor file.
+description: command line tool for CNV/CNA analysis. This step imports the read
+  depth data into a root pytor file.
 keywords:
   - read depth
   - cnv
@@ -13,7 +13,8 @@ tools:
       documentation: https://github.com/abyzovlab/CNVpytor
       tool_dev_url: https://github.com/abyzovlab/CNVpytor
       doi: "10.1101/2021.01.27.428472v1"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:cnvpytor
 input:
   - - meta:
@@ -33,8 +34,8 @@ input:
         ontologies: []
   - fasta:
       type: file
-      description: specifies reference genome file (only for cram file without reference
-        genome)
+      description: specifies reference genome file (only for cram file without
+        reference genome)
       pattern: "*.{fasta,fasta.gz,fa,fa.gz}"
       ontologies: []
   - fai:
@@ -51,17 +52,31 @@ output:
             e.g. [ id:'test' ]
       - "*.pytor":
           type: file
-          description: read depth root file in which read depth data binned to 100 base
-            pair bins will be stored.
+          description: read depth root file in which read depth data binned to 100
+            base pair bins will be stored.
           pattern: "*.{pytor}"
           ontologies: []
+  versions_cnvpytor:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - cnvpytor:
+          type: string
+          description: The name of the tool
+      - 1.3.2:
+          type: string
+          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
+      - cnvpytor:
+          type: string
+          description: The name of the tool
+      - 1.3.2:
+          type: string
+          description: The expression to obtain the version of the tool
 authors:
   - "@sima-r"
   - "@ramprasadn"

modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test

@@ -33,7 +33,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     file(process.out.pytor[0][1]).name,
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )
@@ -62,7 +62,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     file(process.out.pytor[0][1]).name,
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )

modules/nf-core/cnvpytor/importreaddepth/tests/main.nf.test.snap

@@ -2,15 +2,21 @@
     "test-cnvpytor-importreaddepth": {
         "content": [
             "test.pytor",
-            [
-                "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27"
-            ]
+            {
+                "versions_cnvpytor": [
+                    [
+                        "CNVPYTOR_IMPORTREADDEPTH",
+                        "cnvpytor",
+                        "1.3.1"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T13:08:50.744070399",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-28T14:03:16.865191"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "test-cnvpytor-importreaddepth-cram-stub": {
         "content": [
@@ -24,7 +30,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27"
+                    [
+                        "CNVPYTOR_IMPORTREADDEPTH",
+                        "cnvpytor",
+                        "1.3.2"
+                    ]
                 ],
                 "pytor": [
                     [
@@ -34,28 +44,38 @@
                         "test.pytor:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27"
+                "versions_cnvpytor": [
+                    [
+                        "CNVPYTOR_IMPORTREADDEPTH",
+                        "cnvpytor",
+                        "1.3.2"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-13T16:34:42.62061788",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-28T14:03:34.286753"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "test-cnvpytor-importreaddepth-cram": {
         "content": [
             "test.pytor",
-            [
-                "versions.yml:md5,8b48cc59a72c589feb7e51e10f589b27"
-            ]
+            {
+                "versions_cnvpytor": [
+                    [
+                        "CNVPYTOR_IMPORTREADDEPTH",
+                        "cnvpytor",
+                        "1.3.1"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T13:09:01.201749134",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-28T14:03:27.674852"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }