nf-core · ammaraziz · Jul 1, 2026 · Jul 1, 2026 · Jul 1, 2026 · Jul 2, 2026
diff --git a/modules/nf-core/pangolin/run/environment.yml b/modules/nf-core/pangolin/run/environment.yml
@@ -1,8 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 
 dependencies:
-  - bioconda::pangolin=4.3.1
-  - bioconda::pangolin-data=1.32
-  - bioconda::snakemake=7.32.4
+  - bioconda::pangolin-data=1.39
+  - bioconda::pangolin=4.4
+  - bioconda::snakemake-minimal=9.21.1
diff --git a/modules/nf-core/pangolin/run/main.nf b/modules/nf-core/pangolin/run/main.nf
@@ -4,16 +4,16 @@ process PANGOLIN_RUN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f10f9bd63d24e2382406b2b348c65ae1ac74118e6eb17f5e30b310fbc1bc4b9/data' :
-        'community.wave.seqera.io/library/pangolin-data_pangolin_pip_snakemake:7987089a2a044e70' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/85/858e91f6972f0d8d71dae844bf0232656f5d91112b9a5610f559659b33414c86/data' :
+        'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake-minimal:638a1eb68adff9c7' }"
 
     input:
     tuple val(meta), path(fasta)
     path(db)
 
     output:
     tuple val(meta), path('*.csv'), emit: report
-    path  "versions.yml"          , emit: versions
+    tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed 's/pangolin //'"), emit: versions_pangolin, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,11 +31,6 @@ process PANGOLIN_RUN {
         --outfile ${prefix}.pangolin.csv \\
         --threads $task.cpus \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pangolin: \$(pangolin --version | sed "s/pangolin //g")
-    END_VERSIONS
     """
 
     stub:
@@ -44,10 +39,5 @@ process PANGOLIN_RUN {
     export XDG_CACHE_HOME=/tmp/.cache
 
     touch ${prefix}.pangolin.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pangolin: \$(pangolin --version | sed "s/pangolin //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml
@@ -11,7 +11,8 @@ tools:
         Phylogenetic Assignment of Named Global Outbreak LINeages
       homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
       manual: https://github.com/cov-lineages/pangolin#pangolearn-description
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: biotools:pangolin_cov-lineages
 input:
   - - meta:
@@ -27,7 +28,6 @@ input:
       type: directory
       description: |
         Directory containing the Pangolin database
-
 output:
   report:
     - - meta:
@@ -39,14 +39,28 @@ output:
           description: Pangolin lineage report
           pattern: "*.{csv}"
           ontologies:
-            - edam: http://edamontology.org/format_3752 # CSV
+            - edam: http://edamontology.org/format_3752 #CSV
+  versions_pangolin:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pangolin:
+          type: string
+          description: The name of the tool
+      - pangolin -v | sed 's/pangolin //':
+          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
+      - pangolin:
+          type: string
+          description: The name of the tool
+      - pangolin -v | sed 's/pangolin //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@kevinmenden"
   - "@drpatelh"

diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test b/modules/nf-core/pangolin/run/tests/main.nf.test
@@ -61,11 +61,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.report[0][1]).readLines().first().contains("taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note") },
-                { assert snapshot(
-                    file(process.out.report[0][1]).name,
-                    process.out.versions
-                    ).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["report"])).match() }
+
             )
         }
     }

diff --git a/modules/nf-core/pangolin/run/tests/main.nf.test.snap b/modules/nf-core/pangolin/run/tests/main.nf.test.snap
@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e"
+                    [
+                        "PANGOLIN_RUN",
+                        "pangolin",
+                        "4.4"
+                    ]
                 ],
                 "report": [
                     [
@@ -21,29 +25,46 @@
                         "test.pangolin.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e"
+                "versions_pangolin": [
+                    [
+                        "PANGOLIN_RUN",
+                        "pangolin",
+                        "4.4"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-07-20T11:54:15.284245093",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T11:10:47.50504972"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
     },
     "sarscov2 genome [fasta] - update data": {
         "content": [
-            "test.pangolin.csv",
-            [
-                "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e"
-            ]
+            {
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pangolin.csv"
+                    ]
+                ],
+                "versions_pangolin": [
+                    [
+                        "PANGOLIN_RUN",
+                        "pangolin",
+                        "4.4"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-07-20T11:58:12.906874243",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T11:10:27.540927677"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
     },
     "sarscov2 genome [fasta]": {
         "content": [
@@ -53,29 +74,37 @@
                         {
                             "id": "test"
                         },
-                        "test.pangolin.csv:md5,876b3d5cb0f2b438cb62931b81bb0c8c"
+                        "test.pangolin.csv:md5,bdcdb7bcec59c2e6a12c11ac7ce43b09"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e"
+                    [
+                        "PANGOLIN_RUN",
+                        "pangolin",
+                        "4.4"
+                    ]
                 ],
                 "report": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.pangolin.csv:md5,876b3d5cb0f2b438cb62931b81bb0c8c"
+                        "test.pangolin.csv:md5,bdcdb7bcec59c2e6a12c11ac7ce43b09"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3611292dc0d16ab155d60c40b998d57e"
+                "versions_pangolin": [
+                    [
+                        "PANGOLIN_RUN",
+                        "pangolin",
+                        "4.4"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-07-20T11:53:38.602007683",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-25T11:09:22.593905868"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
     }
 }
diff --git a/modules/nf-core/pangolin/updatedata/environment.yml b/modules/nf-core/pangolin/updatedata/environment.yml
@@ -1,8 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 
 dependencies:
-  - bioconda::pangolin=4.3.1
-  - bioconda::pangolin-data=1.32
-  - bioconda::snakemake=7.32.4
+  - bioconda::pangolin-data=1.39
+  - bioconda::pangolin=4.4
+  - bioconda::snakemake-minimal=9.21.1
diff --git a/modules/nf-core/pangolin/updatedata/main.nf b/modules/nf-core/pangolin/updatedata/main.nf
@@ -4,15 +4,16 @@ process PANGOLIN_UPDATEDATA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f10f9bd63d24e2382406b2b348c65ae1ac74118e6eb17f5e30b310fbc1bc4b9/data' :
-        'community.wave.seqera.io/library/pangolin-data_pangolin_pip_snakemake:7987089a2a044e70' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/85/858e91f6972f0d8d71dae844bf0232656f5d91112b9a5610f559659b33414c86/data' :
+        'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake-minimal:638a1eb68adff9c7' }"
 
     input:
     val(dbname)
 
     output:
-    path("${prefix}")   , emit: db
-    path "versions.yml" , emit: versions
+    path("${prefix}")           , emit: db
+    tuple val("${task.process}"), val('pangolin-dataset'), eval("pangolin -pv | sed -n 's/pangolin-data \\([0-9.]*\\).*/\\1/p'"), emit: versions_pangolin_dataset, topic: versions
+    tuple val("${task.process}"), val('pangolin'), eval("pangolin -v | sed 's/pangolin //'"), emit: versions_pangolin, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,21 +30,11 @@ process PANGOLIN_UPDATEDATA {
         --update-data \\
         --threads $task.cpus \\
         --datadir ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pangolin: \$(pangolin --version | sed "s/pangolin //g")
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${dbname}"
     """
     mkdir -p ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pangolin: \$(pangolin --version | sed "s/pangolin //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pangolin/updatedata/meta.yml b/modules/nf-core/pangolin/updatedata/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: pangolin_updatedata
 description: Phylogenetic Assignment of Named Global Outbreak LINeages
 keywords:
@@ -13,9 +12,9 @@ tools:
         Phylogenetic Assignment of Named Global Outbreak LINeages
       homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
       manual: https://github.com/cov-lineages/pangolin#pangolearn-description
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: biotools:pangolin_cov-lineages
-
 input:
   - dbname:
       type: string
@@ -24,17 +23,49 @@ output:
   db:
     - ${prefix}:
         type: file
-        description: Directory containing downloaded data with directory naming being
-          the user provided dbname or prefix.
+        description: Directory containing downloaded data with directory naming
+          being the user provided dbname or prefix.
         ontologies: []
+  versions_pangolin_dataset:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pangolin-dataset:
+          type: string
+          description: The name of the tool
+      - pangolin -pv | sed -n 's/pangolin-data \([0-9.]*\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_pangolin:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pangolin:
+          type: string
+          description: The name of the tool
+      - pangolin -v | sed 's/pangolin //':
+          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
+      - pangolin-dataset:
+          type: string
+          description: The name of the tool/dataset
+      - pangolin -pv | sed -n 's/pangolin-data \([0-9.]*\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pangolin:
+          type: string
+          description: The name of the tool
+      - pangolin -v | sed 's/pangolin //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@Joon-Klaps"
 maintainers:

diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test b/modules/nf-core/pangolin/updatedata/tests/main.nf.test
@@ -23,11 +23,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.db[0].toString()).listFiles().collect { it.name }.toSorted(), // A mix of empty and non-empty files
-                    process.out.versions
-                    ).match()
-                }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["report"])).match() }
             )
         }
     }