From 6f2da6db24e1face9da018d09a0007642f6ca131 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Thu, 30 Apr 2026 17:07:06 -0400
Subject: [PATCH 1/6] feat(mygene): migrate to topic: versions, add stub block,
 sanitizeOutput assertions

---
 modules/nf-core/mygene/main.nf                |  14 +-
 modules/nf-core/mygene/meta.yml               |  27 +-
 modules/nf-core/mygene/tests/main.nf.test     |  35 ++-
 .../nf-core/mygene/tests/main.nf.test.snap    | 287 +++++++++++++-----
 4 files changed, 272 insertions(+), 91 deletions(-)

diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf
index 70141d142f80..1d49dc52f75f 100644
--- a/modules/nf-core/mygene/main.nf
+++ b/modules/nf-core/mygene/main.nf
@@ -13,11 +13,23 @@ process MYGENE {
     output:
     tuple val(meta), path("*.gmt"), emit: gmt
     tuple val(meta), path("*.tsv"), emit: tsv     , optional: true
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions_mygene, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     template "mygene.py"
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gmt
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mygene: \$(python3 -c 'import mygene; print(mygene.__version__)')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml
index 8356c502ef32..363abcf96231 100644
--- a/modules/nf-core/mygene/meta.yml
+++ b/modules/nf-core/mygene/meta.yml
@@ -11,9 +11,9 @@ tools:
       documentation: "https://docs.mygene.info/projects/mygene-py/en/latest/"
       tool_dev_url: "https://github.com/biothings/mygene.py"
       doi: "10.1093/nar/gks1114"
-      licence: ["Apache-2.0"]
+      licence:
+        - "Apache-2.0"
       identifier: biotools:mygene
-
 input:
   - - meta:
         type: map
@@ -22,13 +22,13 @@ input:
           e.g. `[ id:'sample1' ]`
     - gene_list:
         type: file
-        description: A tsv/csv file that contains a list of gene ids in one of the columns.
-          By default, the column name should be "gene_id", but this can be changed by
-          using "--columname gene_id" in ext.args.
+        description: A tsv/csv file that contains a list of gene ids in one of the
+          columns. By default, the column name should be "gene_id", but this can
+          be changed by using "--columname gene_id" in ext.args.
         pattern: "*.{csv,tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3752 # CSV
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3752
+          - edam: http://edamontology.org/format_3475
 output:
   gmt:
     - - meta:
@@ -55,14 +55,23 @@ output:
             query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+
+  versions_mygene:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+topics:
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@suzannejin"
 maintainers:
diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test
index e5ba64caa3b8..6f87bdc8f89f 100644
--- a/modules/nf-core/mygene/tests/main.nf.test
+++ b/modules/nf-core/mygene/tests/main.nf.test
@@ -25,8 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default options - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - default options - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -49,9 +48,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default with tsv file - gmt") },
-                { assert snapshot(process.out.tsv).match("mygene - default with tsv file - tsv") },
-                { assert snapshot(process.out.versions).match("mygene - default with tsv file - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -74,8 +71,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go category - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go category - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -98,8 +94,29 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go evidence - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go evidence - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("mygene - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id : 'test'],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv")
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index d6a334c7ed62..87e019dbe59a 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -1,40 +1,4 @@
 {
-    "mygene - filter by go evidence - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:31.854823"
-    },
-    "mygene - default options - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:19:43.081388"
-    },
-    "mygene - default with tsv file - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.837699"
-    },
     "mygene - default options - gmt": {
         "content": [
             [
@@ -42,27 +6,45 @@
                     {
                         "id": "test"
                     },
-                    "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834"
+                    "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
                 ]
             ]
         ],
+        "timestamp": "2026-04-30T12:11:06.882594",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:19:43.060437"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
-    "mygene - filter by go category - versions": {
+    "mygene - stub": {
         "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
+                ]
+            }
         ],
+        "timestamp": "2026-04-30T16:31:53.563524",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:17.233994"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "mygene - filter by go evidence - gmt": {
         "content": [
@@ -71,65 +53,226 @@
                     {
                         "id": "test"
                     },
-                    "test.gmt:md5,da6b31a5f889e3aedb16b4154f9652af"
+                    "test.gmt:md5,9522f1a93897fb9b1a2b2109cb49baa1"
                 ]
             ]
         ],
+        "timestamp": "2026-04-30T12:11:49.301318",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:31.827798"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
-    "mygene - default with tsv file - tsv": {
+    "mygene - default with tsv file - gmt": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.tsv:md5,018e23173b224cbf328751006593900e"
+                    "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
                 ]
             ]
         ],
+        "timestamp": "2026-04-30T12:11:23.476588",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.81872"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
-    "mygene - default with tsv file - gmt": {
+    "mygene - filter by go category - gmt": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834"
+                    "test.gmt:md5,369d949e20afdb7a1645c7794a078e8b"
                 ]
             ]
         ],
+        "timestamp": "2026-04-30T12:11:36.010332",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.79811"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
-    "mygene - filter by go category - gmt": {
+    "mygene - default options": {
+        "content": [
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T16:31:00.312209",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "mygene - filter by go evidence - versions": {
+        "content": [
+            {
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T12:11:49.322104",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "mygene - default options - versions": {
+        "content": [
+            {
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T12:11:06.905565",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "mygene - default with tsv file - versions": {
+        "content": [
+            {
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T12:11:23.512617",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "mygene - filter by go category - versions": {
+        "content": [
+            {
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T12:11:36.031086",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "mygene - filter by go evidence": {
+        "content": [
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,9522f1a93897fb9b1a2b2109cb49baa1"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T16:31:47.065255",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "mygene - filter by go category": {
+        "content": [
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,369d949e20afdb7a1645c7794a078e8b"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T16:31:32.999049",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "mygene - default with tsv file - tsv": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.gmt:md5,213c1d1d2345df8ea51d67cb1670f4f7"
+                    "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
                 ]
             ]
         ],
+        "timestamp": "2026-04-30T12:11:23.495978",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "mygene - default with tsv file": {
+        "content": [
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
+                    ]
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T16:31:19.012356",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:17.208509"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file

From 214f3d3ec42257dca2bb0b3b0752dff7c794693c Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:01:04 -0400
Subject: [PATCH 2/6] Fix mygene PR feedback: restore EDAM ontologies and
 snapshot versions

---
 modules/nf-core/mygene/meta.yml               |  4 +-
 modules/nf-core/mygene/tests/main.nf.test     | 25 +++++++++---
 .../nf-core/mygene/tests/main.nf.test.snap    | 39 ++++++++++++++++---
 3 files changed, 56 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml
index 363abcf96231..2683c9ee20f9 100644
--- a/modules/nf-core/mygene/meta.yml
+++ b/modules/nf-core/mygene/meta.yml
@@ -27,8 +27,8 @@ input:
           be changed by using "--columname gene_id" in ext.args.
         pattern: "*.{csv,tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3752
-          - edam: http://edamontology.org/format_3475
+          - edam: http://edamontology.org/format_3752 # CSV
+          - edam: http://edamontology.org/format_3475 # TSV
 output:
   gmt:
     - - meta:
diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test
index 6f87bdc8f89f..504e5f8b6beb 100644
--- a/modules/nf-core/mygene/tests/main.nf.test
+++ b/modules/nf-core/mygene/tests/main.nf.test
@@ -25,7 +25,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    path(process.out.versions_mygene[0]).yaml
+                ).match() }
             )
         }
     }
@@ -48,7 +51,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    path(process.out.versions_mygene[0]).yaml
+                ).match() }
             )
         }
     }
@@ -71,7 +77,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    path(process.out.versions_mygene[0]).yaml
+                ).match() }
             )
         }
     }
@@ -94,7 +103,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    path(process.out.versions_mygene[0]).yaml
+                ).match() }
             )
         }
     }
@@ -116,7 +128,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    path(process.out.versions_mygene[0]).yaml
+                ).match() }
             )
         }
     }
diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index 87e019dbe59a..1b629690def7 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -38,9 +38,14 @@
                 "versions_mygene": [
                     "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
                 ]
+            },
+            {
+                "MYGENE": {
+                    "mygene": "3.2.2"
+                }
             }
         ],
-        "timestamp": "2026-04-30T16:31:53.563524",
+        "timestamp": "2026-05-01T07:00:51.636799",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -114,9 +119,15 @@
                 "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
+            },
+            {
+                "MYGENE": {
+                    "argparse": 1.1,
+                    "mygene": "3.2.2"
+                }
             }
         ],
-        "timestamp": "2026-04-30T16:31:00.312209",
+        "timestamp": "2026-05-01T06:57:26.801338",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -195,9 +206,15 @@
                 "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
+            },
+            {
+                "MYGENE": {
+                    "argparse": 1.1,
+                    "mygene": "3.2.2"
+                }
             }
         ],
-        "timestamp": "2026-04-30T16:31:47.065255",
+        "timestamp": "2026-05-01T07:00:17.553057",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -220,9 +237,15 @@
                 "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
+            },
+            {
+                "MYGENE": {
+                    "argparse": 1.1,
+                    "mygene": "3.2.2"
+                }
             }
         ],
-        "timestamp": "2026-04-30T16:31:32.999049",
+        "timestamp": "2026-05-01T06:59:16.231201",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -267,9 +290,15 @@
                 "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
+            },
+            {
+                "MYGENE": {
+                    "argparse": 1.1,
+                    "mygene": "3.2.2"
+                }
             }
         ],
-        "timestamp": "2026-04-30T16:31:19.012356",
+        "timestamp": "2026-05-01T06:58:21.313155",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"

From ed70d299638f5d0206c4a16a3676b779d09d9888 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:12:11 -0400
Subject: [PATCH 3/6] Revert mygene snapshot assertion change

---
 modules/nf-core/mygene/tests/main.nf.test     | 10 +++----
 .../nf-core/mygene/tests/main.nf.test.snap    | 27 ++++++++-----------
 2 files changed, 16 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test
index 504e5f8b6beb..640422c4f9d2 100644
--- a/modules/nf-core/mygene/tests/main.nf.test
+++ b/modules/nf-core/mygene/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    path(process.out.versions_mygene[0]).yaml
+                    process.out.versions[0]
                 ).match() }
             )
         }
@@ -53,7 +53,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    path(process.out.versions_mygene[0]).yaml
+                    process.out.versions[0]
                 ).match() }
             )
         }
@@ -79,7 +79,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    path(process.out.versions_mygene[0]).yaml
+                    process.out.versions[0]
                 ).match() }
             )
         }
@@ -105,7 +105,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    path(process.out.versions_mygene[0]).yaml
+                    process.out.versions[0]
                 ).match() }
             )
         }
@@ -130,7 +130,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    path(process.out.versions_mygene[0]).yaml
+                    process.out.versions[0]
                 ).match() }
             )
         }
diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index 1b629690def7..93598e000372 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions_mygene": [
+                "versions": [
                     "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
                 ]
             },
@@ -45,7 +45,7 @@
                 }
             }
         ],
-        "timestamp": "2026-05-01T07:00:51.636799",
+        "timestamp": "2026-05-01T07:11:07.619668",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -116,18 +116,13 @@
                 "tsv": [
                     
                 ],
-                "versions_mygene": [
+                "versions": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
-            {
-                "MYGENE": {
-                    "argparse": 1.1,
-                    "mygene": "3.2.2"
-                }
-            }
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T06:57:26.801338",
+        "timestamp": "2026-05-01T07:11:58.951091",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -203,7 +198,7 @@
                 "tsv": [
                     
                 ],
-                "versions_mygene": [
+                "versions": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
@@ -214,7 +209,7 @@
                 }
             }
         ],
-        "timestamp": "2026-05-01T07:00:17.553057",
+        "timestamp": "2026-05-01T07:11:01.26946",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -234,7 +229,7 @@
                 "tsv": [
                     
                 ],
-                "versions_mygene": [
+                "versions": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
@@ -245,7 +240,7 @@
                 }
             }
         ],
-        "timestamp": "2026-05-01T06:59:16.231201",
+        "timestamp": "2026-05-01T07:10:46.279333",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -287,7 +282,7 @@
                         "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
                     ]
                 ],
-                "versions_mygene": [
+                "versions": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
@@ -298,7 +293,7 @@
                 }
             }
         ],
-        "timestamp": "2026-05-01T06:58:21.313155",
+        "timestamp": "2026-05-01T07:10:32.622341",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"

From 25600a27f0775caa854057930e43ab94a6047930 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:12:31 -0400
Subject: [PATCH 4/6] Standardize version emission and restore EDAM

---
 modules/nf-core/mygene/main.nf  | 2 +-
 modules/nf-core/mygene/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf
index 1d49dc52f75f..73a90ad793b6 100644
--- a/modules/nf-core/mygene/main.nf
+++ b/modules/nf-core/mygene/main.nf
@@ -13,7 +13,7 @@ process MYGENE {
     output:
     tuple val(meta), path("*.gmt"), emit: gmt
     tuple val(meta), path("*.tsv"), emit: tsv     , optional: true
-    path "versions.yml"           , emit: versions_mygene, topic: versions
+    path "versions.yml"           , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml
index 2683c9ee20f9..d2cea5d8dd7c 100644
--- a/modules/nf-core/mygene/meta.yml
+++ b/modules/nf-core/mygene/meta.yml
@@ -57,7 +57,7 @@ output:
           ontologies:
             - edam: http://edamontology.org/format_3475
 
-  versions_mygene:
+  versions:
     - versions.yml:
         type: file
         description: File containing software versions

From 875c395d062ab61ca71bd9ac727447c180f6b280 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:13:08 -0400
Subject: [PATCH 5/6] Update snapshot after reverting .yaml assertion

---
 .../nf-core/mygene/tests/main.nf.test.snap    | 35 +++++--------------
 1 file changed, 8 insertions(+), 27 deletions(-)

diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index 93598e000372..6197cfcdc54b 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -39,13 +39,9 @@
                     "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
                 ]
             },
-            {
-                "MYGENE": {
-                    "mygene": "3.2.2"
-                }
-            }
+            "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
         ],
-        "timestamp": "2026-05-01T07:11:07.619668",
+        "timestamp": "2026-05-01T07:12:48.586559",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -202,14 +198,9 @@
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
-            {
-                "MYGENE": {
-                    "argparse": 1.1,
-                    "mygene": "3.2.2"
-                }
-            }
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:11:01.26946",
+        "timestamp": "2026-05-01T07:12:43.032465",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -233,14 +224,9 @@
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
-            {
-                "MYGENE": {
-                    "argparse": 1.1,
-                    "mygene": "3.2.2"
-                }
-            }
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:10:46.279333",
+        "timestamp": "2026-05-01T07:12:29.616756",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -286,14 +272,9 @@
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
-            {
-                "MYGENE": {
-                    "argparse": 1.1,
-                    "mygene": "3.2.2"
-                }
-            }
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:10:32.622341",
+        "timestamp": "2026-05-01T07:12:16.653654",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"

From 30d3c0c18cf3d57d8a80c7fb536186ad0483d4cd Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:59:26 -0400
Subject: [PATCH 6/6] =?UTF-8?q?fix(mygene):=20address=20PR=20review=20?=
 =?UTF-8?q?=E2=80=94=20rename=20emit=20to=20versions=5Fmygene,=20update=20?=
 =?UTF-8?q?snapshots?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- main.nf: rename emit: versions to emit: versions_mygene per nf-core convention
- meta.yml: rename output key versions: to versions_mygene: to match emit name
- tests/main.nf.test: update all assertions to process.out.versions_mygene[0]
- tests/main.nf.test.snap: regenerate all 5 snapshots with versions_mygene channel

Addresses review feedback from mribeirodantas on PR #11441.
---
 modules/nf-core/mygene/main.nf                |   2 +-
 modules/nf-core/mygene/meta.yml               |   2 +-
 modules/nf-core/mygene/tests/main.nf.test     |  10 +-
 .../nf-core/mygene/tests/main.nf.test.snap    | 161 ++----------------
 4 files changed, 17 insertions(+), 158 deletions(-)

diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf
index 73a90ad793b6..1d49dc52f75f 100644
--- a/modules/nf-core/mygene/main.nf
+++ b/modules/nf-core/mygene/main.nf
@@ -13,7 +13,7 @@ process MYGENE {
     output:
     tuple val(meta), path("*.gmt"), emit: gmt
     tuple val(meta), path("*.tsv"), emit: tsv     , optional: true
-    path "versions.yml"           , emit: versions, topic: versions
+    path "versions.yml"           , emit: versions_mygene, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml
index d2cea5d8dd7c..2683c9ee20f9 100644
--- a/modules/nf-core/mygene/meta.yml
+++ b/modules/nf-core/mygene/meta.yml
@@ -57,7 +57,7 @@ output:
           ontologies:
             - edam: http://edamontology.org/format_3475
 
-  versions:
+  versions_mygene:
     - versions.yml:
         type: file
         description: File containing software versions
diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test
index 640422c4f9d2..f3b418f44ef6 100644
--- a/modules/nf-core/mygene/tests/main.nf.test
+++ b/modules/nf-core/mygene/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    process.out.versions[0]
+                    process.out.versions_mygene[0]
                 ).match() }
             )
         }
@@ -53,7 +53,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    process.out.versions[0]
+                    process.out.versions_mygene[0]
                 ).match() }
             )
         }
@@ -79,7 +79,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    process.out.versions[0]
+                    process.out.versions_mygene[0]
                 ).match() }
             )
         }
@@ -105,7 +105,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    process.out.versions[0]
+                    process.out.versions_mygene[0]
                 ).match() }
             )
         }
@@ -130,7 +130,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     sanitizeOutput(process.out),
-                    process.out.versions[0]
+                    process.out.versions_mygene[0]
                 ).match() }
             )
         }
diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index 6197cfcdc54b..23a9b58244fd 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -1,21 +1,4 @@
 {
-    "mygene - default options - gmt": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
-                ]
-            ]
-        ],
-        "timestamp": "2026-04-30T12:11:06.882594",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
     "mygene - stub": {
         "content": [
             {
@@ -35,69 +18,18 @@
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
+                "versions_mygene": [
                     "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
                 ]
             },
             "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
         ],
-        "timestamp": "2026-05-01T07:12:48.586559",
+        "timestamp": "2026-05-01T07:52:01.578258",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
         }
     },
-    "mygene - filter by go evidence - gmt": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,9522f1a93897fb9b1a2b2109cb49baa1"
-                ]
-            ]
-        ],
-        "timestamp": "2026-04-30T12:11:49.301318",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
-    "mygene - default with tsv file - gmt": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
-                ]
-            ]
-        ],
-        "timestamp": "2026-04-30T12:11:23.476588",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
-    "mygene - filter by go category - gmt": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,369d949e20afdb7a1645c7794a078e8b"
-                ]
-            ]
-        ],
-        "timestamp": "2026-04-30T12:11:36.010332",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
     "mygene - default options": {
         "content": [
             {
@@ -112,74 +44,18 @@
                 "tsv": [
                     
                 ],
-                "versions": [
+                "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
             "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:11:58.951091",
+        "timestamp": "2026-05-01T07:51:09.551117",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
         }
     },
-    "mygene - filter by go evidence - versions": {
-        "content": [
-            {
-                "versions_mygene": [
-                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-                ]
-            }
-        ],
-        "timestamp": "2026-04-30T12:11:49.322104",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
-    "mygene - default options - versions": {
-        "content": [
-            {
-                "versions_mygene": [
-                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-                ]
-            }
-        ],
-        "timestamp": "2026-04-30T12:11:06.905565",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
-    "mygene - default with tsv file - versions": {
-        "content": [
-            {
-                "versions_mygene": [
-                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-                ]
-            }
-        ],
-        "timestamp": "2026-04-30T12:11:23.512617",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
-    "mygene - filter by go category - versions": {
-        "content": [
-            {
-                "versions_mygene": [
-                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-                ]
-            }
-        ],
-        "timestamp": "2026-04-30T12:11:36.031086",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
     "mygene - filter by go evidence": {
         "content": [
             {
@@ -194,13 +70,13 @@
                 "tsv": [
                     
                 ],
-                "versions": [
+                "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
             "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:12:43.032465",
+        "timestamp": "2026-05-01T07:51:54.816787",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
@@ -220,35 +96,18 @@
                 "tsv": [
                     
                 ],
-                "versions": [
+                "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
             "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:12:29.616756",
+        "timestamp": "2026-05-01T07:51:41.300263",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
         }
     },
-    "mygene - default with tsv file - tsv": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
-                ]
-            ]
-        ],
-        "timestamp": "2026-04-30T12:11:23.495978",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
-        }
-    },
     "mygene - default with tsv file": {
         "content": [
             {
@@ -268,13 +127,13 @@
                         "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
                     ]
                 ],
-                "versions": [
+                "versions_mygene": [
                     "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
             },
             "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
-        "timestamp": "2026-05-01T07:12:16.653654",
+        "timestamp": "2026-05-01T07:51:27.504956",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"