update to new versions capture for checkm2 databasedownload and checkm2 predict

modules/nf-core/checkm2/databasedownload/main.nf

@@ -24,13 +24,17 @@ process CHECKM2_DATABASEDOWNLOAD {
 
     output:
     tuple val(meta), path("checkm2_db_v${db_version}.dmnd"), emit: database
-    path("versions.yml")                                   , emit: versions
+    tuple val("${task.process}"), val('aria2'), eval('aria2c --version 2>&1 | head -n 1 | cut -f3 -d " "'), topic: versions, emit: versions_checkm2_databasedownload
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
+    def args = task.ext.args ?: ''
+    // Append user-agent if not already present
+    if( !args.contains('--user-agent') ) {
+        args = args ? "${args} --user-agent=\"Wget/1.21.4\"" : '--user-agent="Wget/1.21.4"'
+    }
     zenodo_id  = db_zenodo_id ?: 14897628  // Default to version 3 if no ID provided
     api_data   = downloadZenodoApiEntry(zenodo_id)
     db_version = api_data.metadata.version
@@ -48,21 +52,14 @@ process CHECKM2_DATABASEDOWNLOAD {
     db_path=\$(find -name *.dmnd)
     mv \$db_path checkm2_db_v${db_version}.dmnd
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ')
-    END_VERSIONS
+    # cleanup
+    rm -f checkm2_database.tar.gz
     """
 
     stub:
     db_version = 0
     meta       = [id: 'checkm2_db', version: db_version]
     """
     touch checkm2_db_v${db_version}.dmnd
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ')
-    END_VERSIONS
     """
 }

modules/nf-core/checkm2/databasedownload/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "checkm2_databasedownload"
 description: CheckM2 database download
 keywords:
@@ -16,12 +15,10 @@ tools:
       doi: "10.1038/s41592-023-01940-w"
       licence: ["GPL v3"]
       identifier: ""
-
 input:
   - db_zenodo_id:
       type: integer
       description: Zenodo ID of the CheckM2 database to download
-
 output:
   database:
     - - meta:
@@ -34,12 +31,27 @@ output:
           description: CheckM2 database file
           pattern: "checkm2_db_v*.dmnd"
           ontologies: []
+  versions_checkm2_databasedownload:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - aria2:
+          type: string
+          description: The tool name
+      - aria2c --version 2>&1 | head -n 1 | cut -f3 -d " ":
+          type: string
+          description: The command used to generate 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 process the versions were collected from
+      - aria2:
+          type: string
+          description: The tool name
+      - 'aria2c --version 2>&1 | head -n 1 | cut -f3 -d " "':
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@dialvarezs"
+  - "@eit-maxlcummins"

modules/nf-core/checkm2/databasedownload/tests/main.nf.test

@@ -21,7 +21,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.database.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith('versions') }).match() },
             )
         }
 
@@ -42,7 +44,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.database.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith('versions') }).match() },
             )
         }
 

modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap

@@ -1,26 +1,38 @@
 {
     "test_checkm2_databasedownload": {
         "content": [
-            [
-                "versions.yml:md5,74b6560ab3e6bae88ae53cb8ae3c283e"
-            ]
+            {
+                "versions_checkm2_databasedownload": [
+                    [
+                        "CHECKM2_DATABASEDOWNLOAD",
+                        "aria2",
+                        "1.37.0"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-13T21:41:14.428719466"
+        "timestamp": "2026-01-23T09:04:29.73758792"
     },
     "test_checkm2_databasedownload - stub": {
         "content": [
-            [
-                "versions.yml:md5,74b6560ab3e6bae88ae53cb8ae3c283e"
-            ]
+            {
+                "versions_checkm2_databasedownload": [
+                    [
+                        "CHECKM2_DATABASEDOWNLOAD",
+                        "aria2",
+                        "1.37.0"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-13T21:41:24.118075242"
+        "timestamp": "2026-01-29T15:49:13.916311854"
     }
 }

modules/nf-core/checkm2/predict/main.nf

@@ -3,18 +3,18 @@ process CHECKM2_PREDICT {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0af812c983aeffc99c0fca9ed2c910816b2ddb9a9d0dcad7b87dab0c9c08a16f/data'
-        : 'community.wave.seqera.io/library/checkm2:1.1.0--60f287bc25d7a10d'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0a/0af812c983aeffc99c0fca9ed2c910816b2ddb9a9d0dcad7b87dab0c9c08a16f/data':
+        'community.wave.seqera.io/library/checkm2:1.1.0--60f287bc25d7a10d' }"
 
     input:
     tuple val(meta), path(fasta, stageAs: "input_bins/*")
     tuple val(dbmeta), path(db)
 
     output:
-    tuple val(meta), path("${prefix}"), emit: checkm2_output
+    tuple val(meta), path("${prefix}")                   , emit: checkm2_output
     tuple val(meta), path("${prefix}_checkm2_report.tsv"), emit: checkm2_tsv
-    path ("versions.yml"), emit: versions
+    tuple val("${task.process}"), val('checkm2'), eval('checkm2 --version'), topic: versions, emit: versions_checkm2_predict
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,33 +23,21 @@ process CHECKM2_PREDICT {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    export DB=\$(find -L . -name "*.dmnd" -type f)
-
     checkm2 \\
         predict \\
         --input ${fasta} \\
         --output-directory ${prefix} \\
         --threads ${task.cpus} \\
-        --database_path \$DB \\
+        --database_path ${db} \\
         ${args}
 
     cp ${prefix}/quality_report.tsv ${prefix}_checkm2_report.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        checkm2: \$(checkm2 --version)
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir ${prefix}/
     touch ${prefix}_checkm2_report.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        checkm2: \$(checkm2 --version)
-    END_VERSIONS
     """
 }

modules/nf-core/checkm2/predict/meta.yml

@@ -16,7 +16,6 @@ tools:
       doi: "10.1038/s41592-023-01940-w"
       licence: ["GPL v3"]
       identifier: ""
-
 input:
   - - meta:
         type: map
@@ -37,6 +36,7 @@ input:
         type: file
         description: CheckM2 database
         ontologies: []
+
 output:
   checkm2_output:
     - - meta:
@@ -60,12 +60,27 @@ output:
           pattern: "*.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_checkm2_predict:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - checkm2:
+          type: string
+          description: The name of the tool
+      - "checkm2 --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 process the versions were collected from
+      - checkm2:
+          type: string
+          description: The tool name
+      - "checkm2 --version":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@dialvarezs"
+  - "@eit-maxlcummins"

modules/nf-core/checkm2/predict/tests/main.nf.test

@@ -5,18 +5,16 @@ nextflow_process {
     tag "modules"
     tag "checkm2"
     tag "checkm2/predict"
-    tag "untar"
+    tag "checkm2/databasedownload"
     script "modules/nf-core/checkm2/predict/main.nf"
     process "CHECKM2_PREDICT"
 
     setup {
-            run("UNTAR") {
-                script "../../../untar/main.nf"
+            run("CHECKM2_DATABASEDOWNLOAD") {
+                script "../../databasedownload/main.nf"
                 process {
                     """
-                    input[0] = channel
-                        .fromPath("https://zenodo.org/records/14897628/files/checkm2_database.tar.gz", checkIfExists: true)
-                        .map { dbfile -> [ [id: 'checkm2db'], dbfile ] }
+                    input[0] = []
                     """
                 }
             }
@@ -31,15 +29,15 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)] ]
-                input[1] = UNTAR.out.untar
+                input[1] = CHECKM2_DATABASEDOWNLOAD.out.database
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.checkm2_tsv, process.out.versions).match() }
+                { assert snapshot(process.out.checkm2_tsv, process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -55,15 +53,15 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/prokaryotes/escherichia_coli/genome/genome.fa', checkIfExists: true)] ]
-                input[1] = UNTAR.out.untar
+                input[1] = CHECKM2_DATABASEDOWNLOAD.out.database
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.checkm2_tsv, process.out.versions).match() }
+                { assert snapshot(process.out.checkm2_tsv, process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }

modules/nf-core/checkm2/predict/tests/main.nf.test.snap

@@ -9,15 +9,21 @@
                     "test_checkm2_report.tsv:md5,1b6021262d336b21f526d8369f6ddd3f"
                 ]
             ],
-            [
-                "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195"
-            ]
+            {
+                "versions_checkm2_predict": [
+                    [
+                        "CHECKM2_PREDICT",
+                        "checkm2",
+                        "1.1.0"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-13T15:23:26.857419645"
+        "timestamp": "2026-01-30T09:44:45.556228913"
     },
     "test_checkm2_predict - stub": {
         "content": [
@@ -29,14 +35,20 @@
                     "test_checkm2_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
-            [
-                "versions.yml:md5,f13e02312d6a08ca746e6de2659d8195"
-            ]
+            {
+                "versions_checkm2_predict": [
+                    [
+                        "CHECKM2_PREDICT",
+                        "checkm2",
+                        "1.1.0"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-13T15:23:40.153127645"
+        "timestamp": "2026-01-23T09:28:10.0910672"
     }
 }