feat(maltextract): add stub block and migrate to topic channel versions

modules/nf-core/ectyper/tests/main.nf.test.snap

@@ -21,5 +21,21 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-28T12:49:29.892782"
+    },
+    "versions": {
+        "content": [
+            [
+                [
+                    "ECTYPER",
+                    "ectyper",
+                    "1.0.0"
+                ]
+            ]
+        ],
+        "timestamp": "2024-08-28T12:49:29.892782",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        }
     }
-}
+}

modules/nf-core/maltextract/main.nf

@@ -14,7 +14,7 @@ process MALTEXTRACT {
 
     output:
     tuple val(meta), path("results")      , emit: results
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('maltextract'), eval('MaltExtract --help | head -n 2 | tail -n 1 | sed \'s/MaltExtract version//\''), emit: versions_maltextract, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,10 +30,10 @@ process MALTEXTRACT {
         -r $ncbi_dir \\
         -o results/ \\
         $args
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        maltextract: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
-    END_VERSIONS
+    stub:
+    """
+    mkdir -p results
     """
 }

modules/nf-core/maltextract/meta.yml

@@ -1,6 +1,6 @@
 name: maltextract
-description: Tool for evaluation of MALT results for true positives of ancient metagenomic
-  taxonomic screening
+description: Tool for evaluation of MALT results for true positives of ancient
+  metagenomic taxonomic screening
 keywords:
   - malt
   - MaltExtract
@@ -22,7 +22,8 @@ tools:
       documentation: https://github.com/rhuebler/hops
       tool_dev_url: https://github.com/rhuebler/hops
       doi: "10.1186/s13059-019-1903-0"
-      licence: ["GPL 3"]
+      licence:
+        - "GPL 3"
       identifier: ""
 input:
   - - meta:
@@ -54,13 +55,28 @@ output:
           type: directory
           description: Directory containing MaltExtract text results files
           pattern: "results/"
+
+  versions_maltextract:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - maltextract:
+          type: string
+          description: The name of the tool
+      - MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract 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
+      - maltextract:
+          type: string
+          description: The name of the tool
+      - MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jfy133"
 maintainers:

modules/nf-core/maltextract/tests/main.nf.test

@@ -37,9 +37,36 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
-                    path("${process.out.results.get(0).get(1)}/ScanSummary.txt")
-                ).match() },
+                    path("${process.out.results.get(0).get(1)}/ScanSummary.txt"),
+                    path("${process.out.results.get(0).get(1)}/error.txt").text == "",
+                    path("${process.out.results.get(0).get(1)}/log.txt"),
+                    process.out.versions_maltextract
+                ).match() }
+            )
+        }
+    }
+
+    test("test_maltextract - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/malt/test.rma6')
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/maltextract/taxon_list.txt')
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
+                { assert snapshot(process.out.versions_maltextract).match("versions") }
             )
         }
     }

modules/nf-core/maltextract/tests/main.nf.test.snap

@@ -1,15 +1,61 @@
 {
+    "test_maltextract - stub": {
+        "content": [
+            {
+                "results": [
+                    [
+                        [],
+                        []
+                    ]
+                ],
+                "versions_maltextract": [
+                    [
+                        "MALTEXTRACT",
+                        "maltextract",
+                        "1.7"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T22:34:21.854841",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
     "test_maltextract": {
+        "content": [
+            "ScanSummary.txt:md5,209fb35426f6a459db0f4af0dc544b10",
+            true,
+            "log.txt:md5,7d1a25809c8c92b550a43773fc78cfd4",
+            [
+                [
+                    "MALTEXTRACT",
+                    "maltextract",
+                    "1.7"
+                ]
+            ]
+        ],
+        "timestamp": "2026-04-29T22:33:46.095165",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "versions": {
         "content": [
             [
-                "versions.yml:md5,4d87de5def1287321effde6545901cf6"
-            ],
-            "ScanSummary.txt:md5,209fb35426f6a459db0f4af0dc544b10"
+                [
+                    "MALTEXTRACT",
+                    "maltextract",
+                    "1.7"
+                ]
+            ]
         ],
+        "timestamp": "2026-04-29T22:34:21.854841",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-07-01T08:19:20.696046683"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
-}
+}

modules/nf-core/optitype/tests/main.nf.test.snap

@@ -74,5 +74,21 @@
             "nextflow": "23.10.1"
         },
         "timestamp": "2024-03-06T13:50:18.885995054"
+    },
+    "versions": {
+        "content": [
+            [
+                [
+                    "OPTITYPE",
+                    "optitype",
+                    "1.3.1"
+                ]
+            ]
+        ],
+        "timestamp": "2024-03-06T13:47:07.297380921",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        }
     }
-}
+}

modules/nf-core/prinseqplusplus/tests/main.nf.test.snap

@@ -2,9 +2,7 @@
     "test-prinseqplusplus-single-end": {
         "content": [
             "test_good_out.fastq.gz",
-            [
-
-            ],
+            [],
             [
                 [
                     {
@@ -57,5 +55,17 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-27T14:57:53.505032"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,366e108ac2695a852af440e61fecad5e"
+            ]
+        ],
+        "timestamp": "2024-08-27T14:55:34.731661",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        }
     }
-}
+}

modules/nf-core/shasta/tests/main.nf.test.snap

@@ -13,5 +13,21 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-08-23T11:50:23.581975"
+    },
+    "versions": {
+        "content": [
+            [
+                [
+                    "SHASTA",
+                    "shasta",
+                    "0.8.0"
+                ]
+            ]
+        ],
+        "timestamp": "2024-08-23T11:50:23.581975",
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        }
     }
-}
+}