nf-core · SPPearce · Jul 15, 2026 · Jul 15, 2026 · Jul 15, 2026 · Jul 15, 2026
diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf
@@ -13,12 +13,24 @@ process PROPR_GREA {
 
     output:
     tuple val(meta), path("*.grea.tsv"), emit: results
-    path "versions.yml",                 emit: versions
+    path "versions.yml",                 emit: versions, topic: versions
     path "*.R_sessionInfo.log",          emit: session_info
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     template 'grea.R'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.grea.tsv
+    touch ${prefix}.R_sessionInfo.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-propr: \$(Rscript -e "cat(as.character(packageVersion('propr')))")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "propr_grea"
 description: Perform Gene Ratio Enrichment Analysis
 keywords:
@@ -15,7 +14,8 @@ tools:
       documentation: "https://rdrr.io/cran/propr/man/propr.html"
       tool_dev_url: "https://github.com/tpq/propr"
       doi: "10.2202/1544-6115.1175"
-      licence: ["GPL-2"]
+      licence:
+        - "GPL-2"
       identifier: biotools:propr
 input:
   - - meta:
@@ -77,6 +77,11 @@ output:
         description: dump of R SessionInfo
         pattern: "*.R_sessionInfo.log"
         ontologies: []
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@caraiz2001"
   - "@suzannejin"

diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test
@@ -9,11 +9,10 @@ nextflow_process {
     tag "propr"
     tag "propr/grea"
     tag "propr/propd"
+    config "./nextflow.config"
 
     test("test grea chained to propd") {
-
-        tag "default"
-        config "./grea_test.config"
+
 
         setup {
             run("PROPR_PROPD") {
@@ -57,9 +56,29 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.results,
-                    process.out.versions
-                ).match()}
+                    sanitizeOutput(process.out),
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+    }
+
+    test("test grea chained to propd - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [[ id: 'test' ], []]
+                input[1] = [[ id: 'test' ], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap
@@ -1,26 +1,61 @@
 {
+    "test grea chained to propd - stub": {
+        "content": [
+            {
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "session_info": [
+                    "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba"
+                ]
+            }
+        ],
+        "timestamp": "2026-07-15T09:39:18.036935358",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
     "test grea chained to propd": {
         "content": [
-            [
-                [
-                    {
-                        "id": "treatment_mCherry_hND6_",
-                        "variable": "treatment",
-                        "reference": "mCherry",
-                        "target": "hND6",
-                        "blocking": ""
-                    },
-                    "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697"
+            {
+                "results": [
+                    [
+                        {
+                            "id": "treatment_mCherry_hND6_",
+                            "variable": "treatment",
+                            "reference": "mCherry",
+                            "target": "hND6",
+                            "blocking": ""
+                        },
+                        "treatment_mCherry_hND6_.grea.tsv:md5,d685990740bdf74a554d18f7c5f73f4a"
+                    ]
+                ],
+                "session_info": [
+                    "treatment_mCherry_hND6_.R_sessionInfo.log:md5,e9e64218c010b1b04ea818b92b3f3f60"
+                ],
+                "versions": [
+                    "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba"
                 ]
-            ],
-            [
-                "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba"
-            ]
+            },
+            {
+                "PROPR_GREA": {
+                    "r-propr": "5.1.5"
+                }
+            }
         ],
+        "timestamp": "2026-07-15T10:31:30.880768792",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-11T13:00:02.026244403"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
-}
+}
diff --git a/...nf-core/propr/grea/tests/grea_test.config → .../nf-core/propr/grea/tests/nextflow.config b/...nf-core/propr/grea/tests/grea_test.config → .../nf-core/propr/grea/tests/nextflow.config
diff --git a/modules/nf-core/propr/logratio/main.nf b/modules/nf-core/propr/logratio/main.nf
@@ -13,7 +13,7 @@ process PROPR_LOGRATIO {
     output:
     tuple val(meta), path("*.logratio.tsv")     , emit: logratio
     tuple val(meta), path("*.R_sessionInfo.log"), emit: session_info
-    path "versions.yml"                         , emit: versions
+    path "versions.yml"                         , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +22,7 @@ process PROPR_LOGRATIO {
     template 'logratio.R'
 
     stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.logratio.tsv
     touch ${prefix}.R_sessionInfo.log

diff --git a/modules/nf-core/propr/logratio/meta.yml b/modules/nf-core/propr/logratio/meta.yml
@@ -1,6 +1,6 @@
 name: "propr_logratio"
-description: Transform the data matrix using centered logratio transformation (CLR)
-  or additive logratio transformation (ALR)
+description: Transform the data matrix using centered logratio transformation
+  (CLR) or additive logratio transformation (ALR)
 keywords:
   - alr
   - clr
@@ -15,7 +15,8 @@ tools:
       documentation: "https://rdrr.io/cran/propr/man/propr.html"
       tool_dev_url: "https://github.com/tpq/propr"
       doi: "10.1038/s41598-017-16520-0"
-      licence: ["GPL-2"]
+      licence:
+        - "GPL-2"
       identifier: biotools:propr
 input:
   - - meta:
@@ -44,8 +45,8 @@ output:
             [id: 'test', ...]
       - "*.logratio.tsv":
           type: file
-          description: ALR/CLR transformed data matrix. With rows = variables or genes,
-            columns = samples or cells.
+          description: ALR/CLR transformed data matrix. With rows = variables or
+            genes, columns = samples or cells.
           pattern: "*.logratio.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
@@ -68,6 +69,11 @@ output:
         pattern: "versions.yml"
         ontologies:
           - edam: http://edamontology.org/format_3750 # YAML
+topics:
+  versions:
+    - versions.yml:
+        type: string
+        description: The name of the process
 authors:
   - "@suzannejin"
   - "@oprana22"

diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test b/modules/nf-core/propr/logratio/tests/main.nf.test
@@ -226,4 +226,25 @@ nextflow_process {
             )
         }
     }
+
+    test("mus_musculus - tsv - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test'],
+                    []
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test.snap b/modules/nf-core/propr/logratio/tests/main.nf.test.snap
@@ -13,11 +13,31 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T15:13:57.762737802",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T15:13:57.762737802"
+        }
+    },
+    "mus_musculus - tsv - stub": {
+        "content": [
+            {
+                "logratio": [
+
+                ],
+                "session_info": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "timestamp": "2026-07-15T10:21:55.800115714",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "mus_musculus - tsv": {
         "content": [
@@ -40,11 +60,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:35:35.018714127",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:35:35.018714127"
+        }
     },
     "mus_musculus - tsv - alr": {
         "content": [
@@ -67,11 +87,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:42:35.397794344",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:42:35.397794344"
+        }
     },
     "mus_musculus - tsv - alr boxcox": {
         "content": [
@@ -94,11 +114,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:42:43.698056253",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:42:43.698056253"
+        }
     },
     "mus_musculus - tsv -- stub": {
         "content": [
@@ -149,11 +169,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:37:59.786809211",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:37:59.786809211"
+        }
     },
     "mus_musculus - tsv - boxcox": {
         "content": [
@@ -176,11 +196,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:42:28.01694316",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:42:28.01694316"
+        }
     },
     "mus_musculus - tsv - alr geneid": {
         "content": [
@@ -203,11 +223,11 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:42:51.186760616",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:42:51.186760616"
+        }
     },
     "mus_musculus - tsv - alr genename": {
         "content": [
@@ -230,10 +250,10 @@
                 }
             }
         ],
+        "timestamp": "2025-05-16T14:42:58.184822937",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-16T14:42:58.184822937"
+        }
     }
 }