Update to topics getorganelle/*

modules/nf-core/getorganelle/config/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::getorganelle=1.7.7.0
+  - bioconda::getorganelle=1.7.7.1

modules/nf-core/getorganelle/config/main.nf

@@ -3,16 +3,16 @@ process GETORGANELLE_CONFIG {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.0--pyh7cba7a3_0':
-        'quay.io/biocontainers/getorganelle:1.7.7.0--pyh7cba7a3_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.1--pyhdfd78af_0'
+        : 'quay.io/biocontainers/getorganelle:1.7.7.1--pyhdfd78af_0'}"
 
     input:
     val(organelle_type)
 
     output:
     tuple val(organelle_type), path("getorganelle"), emit: db
-    path "versions.yml"                            , emit: versions
+    tuple val("${task.process}"), val('getorganelle'), eval("get_organelle_config.py --version |& sed 's/^GetOrganelle v//'"), topic: versions, emit: versions_getorganelle
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,25 +21,14 @@ process GETORGANELLE_CONFIG {
     def args = task.ext.args ?: ''
     """
     get_organelle_config.py \\
-        $args \\
+        ${args} \\
         -a ${organelle_type} \\
         --config-dir getorganelle
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        getorganelle: \$(get_organelle_config.py --version | sed 's/^GetOrganelle v//g')
-    END_VERSIONS
     """
 
     stub:
-
     """
     mkdir -p getorganelle/{LabelDatabase,SeedDatabase}
     touch getorganelle/{LabelDatabase,SeedDatabase}/${organelle_type}.fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        getorganelle: \$(get_organelle_config.py --version | sed 's/^GetOrganelle v//g')
-    END_VERSIONS
     """
 }

modules/nf-core/getorganelle/config/meta.yml

@@ -13,9 +13,9 @@ tools:
       documentation: "https://github.com/Kinggerm/GetOrganelle"
       tool_dev_url: "https://github.com/Kinggerm/GetOrganelle"
       doi: "10.1186/s13059-020-02154-5"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:getorganelle
-
 input:
   - organelle_type:
       type: string
@@ -30,12 +30,26 @@ output:
       - getorganelle:
           type: directory
           description: Downloaded database for GetOrganelle
+  versions_getorganelle:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - getorganelle:
+          type: string
+          description: Downloaded database for GetOrganelle
+      - get_organelle_config.py --version |& sed 's/^GetOrganelle v//':
+          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
+      - getorganelle:
+          type: string
+          description: Downloaded database for GetOrganelle
+      - get_organelle_config.py --version |& sed 's/^GetOrganelle v//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@erinyoung"

modules/nf-core/getorganelle/config/tests/main.nf.test

@@ -15,7 +15,6 @@ nextflow_process {
             process {
                 """
                 input[0] = 'all'
-
                 """
             }
         }
@@ -24,25 +23,13 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 {
-                    def all_files = []
-
-                    file(process.out.db[0][1]).eachFileRecurse (FileType.FILES) { file ->
-                        all_files << file
-                    }
-
-                    def all_file_names = all_files.collect { it.name }.toSorted()
-
-                    def stable_file_names = [
-                        'VERSION',
-                        'animal_mt.fasta'
-                    ]
-
-                    def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()
+                    def stable_name = getAllFilesFromDir(process.out.db[0][1].toString(), include:['*', '**/*'])
+                    def stable_content = getAllFilesFromDir(process.out.db[0][1].toString(), include:["**/VERSION", "**/animal_mt.fasta"])
 
                     assert snapshot(
-                        all_file_names,
-                        stable_files,
-                        process.out.versions[0]
+                        stable_name*.name.sort(),
+                        stable_content,
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )
@@ -55,15 +42,14 @@ nextflow_process {
             process {
                 """
                 input[0] = 'all'
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/getorganelle/config/tests/main.nf.test.snap

@@ -2,7 +2,7 @@
     "test-getorganelle-config-stub": {
         "content": [
             {
-                "0": [
+                "db": [
                     [
                         "all",
                         [
@@ -15,32 +15,20 @@
                         ]
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
-                ],
-                "db": [
+                "versions_getorganelle": [
                     [
-                        "all",
-                        [
-                            [
-                                "all.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ],
-                            [
-                                "all.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ]
-                        ]
+                        "GETORGANELLE_CONFIG",
+                        "getorganelle",
+                        "1.7.7.1"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
                 ]
             }
         ],
+        "timestamp": "2026-05-07T13:18:22.471441535",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-02T12:42:17.160676"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "test-getorganelle-config": {
         "content": [
@@ -166,12 +154,20 @@
                 "VERSION:md5,f3d5d8493c18ca2e553a6012d1505310",
                 "animal_mt.fasta:md5,2833e57f91c231bd19d678d869ed05df"
             ],
-            "versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
+            {
+                "versions_getorganelle": [
+                    [
+                        "GETORGANELLE_CONFIG",
+                        "getorganelle",
+                        "1.7.7.1"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-05-07T13:49:20.038930564",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-02T13:02:45.095312"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }

modules/nf-core/getorganelle/fromreads/main.nf

@@ -4,18 +4,17 @@ process GETORGANELLE_FROMREADS {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.0--pyh7cba7a3_0'
-        : 'quay.io/biocontainers/getorganelle:1.7.7.0--pyh7cba7a3_0'}"
+        ? 'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.1--pyhdfd78af_0'
+        : 'quay.io/biocontainers/getorganelle:1.7.7.1--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(fastq)
     tuple val(organelle_type), path(db)
 
     output:
     tuple val(meta), path("results/${prefix}.${organelle_type}.fasta.gz"), emit: fasta, optional: true
-    path "results/*", emit: etc
-    // the rest of the result files
-    tuple val("${task.process}"), val('getorganelle_from_reads'), eval("get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'"), topic: versions, emit: versions_getorganelle
+    tuple val(meta), path("results/*"), emit: etc
+    tuple val("${task.process}"), val('getorganelle'), eval("get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//'"), topic: versions, emit: versions_getorganelle
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,6 +48,6 @@ process GETORGANELLE_FROMREADS {
     mkdir results
     touch results/test_1.fastq
     touch results/test_2.fastq
-    echo ''| gzip > results/${prefix}.${organelle_type}.fasta.gz
+    echo "" | gzip > results/${prefix}.${organelle_type}.fasta.gz
     """
 }

modules/nf-core/getorganelle/fromreads/meta.yml

@@ -12,9 +12,9 @@ tools:
       documentation: "https://github.com/Kinggerm/GetOrganelle"
       tool_dev_url: "https://github.com/Kinggerm/GetOrganelle"
       doi: "10.1186/s13059-020-02154-5"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:getorganelle
-
 input:
   - - meta:
         type: map
@@ -45,31 +45,36 @@ output:
           description: Complete or partial organelle sequences
           pattern: "*.fasta.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989 # GZIP
   etc:
-    - results/*:
-        type: file
-        description: Other output files
-        ontologies: []
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - results/*:
+          type: file
+          description: Other output files
+          ontologies: []
   versions_getorganelle:
     - - ${task.process}:
           type: string
           description: The name of the process
-      - getorganelle_from_reads:
+      - getorganelle:
           type: string
           description: The name of the tool
-      - "get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'":
+      - get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
           description: The name of the process
-      - getorganelle_from_reads:
+      - getorganelle:
           type: string
           description: The name of the tool
-      - "get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'":
+      - get_organelle_from_reads.py --version |& sed 's/^GetOrganelle v//':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

modules/nf-core/getorganelle/fromreads/tests/main.nf.test

@@ -25,27 +25,21 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = GETORGANELLE_CONFIG.out.db
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.etc[0][0],
-                    process.out.etc[0][1],
-                    process.out.etc.flatten().collect { file(it).name }.sort(),
-                    process.out.fasta,
-                    process.out.findAll { key, val -> key.startsWith('versions') }).match('main_output') },
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["etc"])).match() },
             )
         }
 
@@ -57,35 +51,25 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ],
                     [
-                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = [
                     'animal_mt',
                     file('mock/getorganelle')
                 ]
-
                 """
             }
         }
 
         then {
-            def fileList_results = process.out.etc.flatten().collect { file(it).name }.sort()
-            def fileList_fasta = file(process.out.fasta[0][1]).name
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                        fileList_results,
-                        fileList_fasta,
-                        process.out.findAll { key, val -> key.startsWith('versions') }
-                    ).match('file_list') }
-
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
-
 }