Linting cleanup of modules starting G

modules/nf-core/ganon/buildcustom/main.nf

@@ -43,10 +43,7 @@ process GANON_BUILDCUSTOM {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def taxonomy_args = taxonomy_files ? "--taxonomy-files ${taxonomy_files}" : ""
-    def genome_size_args = genome_size_files ? "--genome-size-files ${genome_size_files}" : ""
     """
     touch ${prefix}.hibf
     touch ${prefix}.tax

modules/nf-core/ganon/buildcustom/tests/main.nf.test.snap

@@ -3,17 +3,17 @@
         "content": [
             [
                 "test.hibf:md5,9edfe4c3873d621a88ebcad438dca42c",
-                "test.tax:md5,e15400a1e43cce61545834695da46465"
+                "test.tax:md5,5fd3dd6f618d01b33d2ad1c3884aba1d"
             ],
             [
                 "versions.yml:md5,9c73293ae36914c6ce3718ad6728ad9e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2024-11-13T13:37:14.320278404"
+        "timestamp": "2026-02-12T16:23:58.93227895"
     },
     "sarscov2 - genome - fasta": {
         "content": [

modules/nf-core/ganon/classify/main.nf

@@ -45,9 +45,7 @@ process GANON_CLASSIFY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}"
     """
     touch ${prefix}.tre
     touch ${prefix}.rep

modules/nf-core/ganon/classify/tests/main.nf.test.snap

@@ -132,7 +132,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.tre:md5,66c0b9ed247989682fe3bae842d37a76"
+                    "test.tre:md5,2eebb02e0e37268314d41cc274ec3aa0"
                 ]
             ],
             [
@@ -149,10 +149,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2024-10-07T19:26:16.339673954"
+        "timestamp": "2026-02-12T16:28:48.997560554"
     },
     "sarscov2 single-end [fastq]": {
         "content": [
@@ -162,7 +162,7 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.tre:md5,3d2ef6fe0571d7aa7324539407a59630"
+                    "test.tre:md5,828f3ea0e15ae28d95f71ae4874edc38"
                 ]
             ],
             [
@@ -179,9 +179,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2024-10-07T19:25:41.074523387"
+        "timestamp": "2026-02-12T16:28:13.106272473"
     }
 }

modules/nf-core/ganon/report/main.nf

@@ -38,7 +38,6 @@ process GANON_REPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/ganon/report/tests/main.nf.test.snap

@@ -43,7 +43,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tre:md5,3d2ef6fe0571d7aa7324539407a59630"
+                        "test.tre:md5,828f3ea0e15ae28d95f71ae4874edc38"
                     ]
                 ],
                 "1": [
@@ -55,7 +55,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tre:md5,3d2ef6fe0571d7aa7324539407a59630"
+                        "test.tre:md5,828f3ea0e15ae28d95f71ae4874edc38"
                     ]
                 ],
                 "versions": [
@@ -64,9 +64,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2024-10-07T18:32:50.997968794"
+        "timestamp": "2026-02-12T16:25:39.539455533"
     }
 }

modules/nf-core/ganon/table/main.nf

@@ -33,7 +33,6 @@ process GANON_TABLE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/ganon/table/tests/main.nf.test.snap

@@ -40,7 +40,7 @@
                         {
                             "id": "db1"
                         },
-                        "db1.txt:md5,c2f38e9f47f8701d8f37a59dffed88a3"
+                        "db1.txt:md5,1da6f44d95981cca78a50b32d19f2337"
                     ]
                 ],
                 "1": [
@@ -51,7 +51,7 @@
                         {
                             "id": "db1"
                         },
-                        "db1.txt:md5,c2f38e9f47f8701d8f37a59dffed88a3"
+                        "db1.txt:md5,1da6f44d95981cca78a50b32d19f2337"
                     ]
                 ],
                 "versions": [
@@ -60,9 +60,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2024-10-07T18:33:41.271256635"
+        "timestamp": "2026-02-12T16:26:46.650041698"
     }
 }

modules/nf-core/gappa/examineassign/main.nf

@@ -41,7 +41,6 @@ process GAPPA_EXAMINEASSIGN {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.profile.tsv

modules/nf-core/gappa/examineheattree/main.nf

@@ -44,7 +44,6 @@ process GAPPA_EXAMINEHEATTREE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.colours.txt

modules/nf-core/gappa/examineheattree/tests/nextflow.config

@@ -1,6 +1,5 @@
 process {
     withName: 'GAPPA_EXAMINEHEATTREE' {
         ext.args = "--write-newick-tree --write-nexus-tree --write-phyloxml-tree --write-svg-tree"
-        prefix   = { "${meta.id}.heat-tree." }
     }
 }

modules/nf-core/gem2/gemindexer/main.nf

@@ -38,7 +38,6 @@ process GEM2_GEMINDEXER {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 

modules/nf-core/gem3/gem3indexer/main.nf

@@ -37,7 +37,6 @@ process GEM3_GEM3INDEXER {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/genotyphi/parse/main.nf

@@ -18,7 +18,6 @@ process GENOTYPHI_PARSE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/geofetch/main.nf

@@ -33,7 +33,6 @@ process GEOFETCH {
     """
 
     stub:
-    def args = task.ext.args ?: ''
 
     """
     mkdir -p ${geo_accession}

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

@@ -32,7 +32,7 @@ process GETORGANELLE_CONFIG {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+
     """
     mkdir -p getorganelle/{LabelDatabase,SeedDatabase}
     touch getorganelle/{LabelDatabase,SeedDatabase}/${organelle_type}.fasta

modules/nf-core/gfatools/gfa2fa/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gfatools=0.5
+  - bioconda::gfatools=0.5=h577a1d6_5

modules/nf-core/gfatools/gfa2fa/main.nf

@@ -4,15 +4,15 @@ process GFATOOLS_GFA2FA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gfatools:0.5--he4a0461_4':
-        'biocontainers/gfatools:0.5--he4a0461_4' }"
+        'https://depot.galaxyproject.org/singularity/gfatools:0.5--h577a1d6_5':
+        'biocontainers/gfatools:0.5--h577a1d6_5' }"
 
     input:
     tuple val(meta), path(gfa)
 
     output:
     tuple val(meta), path("*.fasta.gz"), emit: fasta
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('gfatools'), eval("gfatools version | sed '1!d; s/.* //'"), topic: versions, emit: versions_gfatools
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,22 +26,11 @@ process GFATOOLS_GFA2FA {
         $args \\
         $gfa \\
         | gzip -c > ${prefix}.fasta.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gfatools: \$( gfatools version | sed '1!d; s/.* //' )
-    END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo | gzip > ${prefix}.fasta.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gfatools: \$( gfatools version | sed '1!d; s/.* //' )
-    END_VERSIONS
     """
 }

modules/nf-core/gfatools/gfa2fa/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "gfatools_gfa2fa"
 description: Converts GFA or rGFA files to FASTA
 keywords:
@@ -15,7 +14,8 @@ tools:
       documentation: "https://github.com/lh3/gfatools"
       tool_dev_url: "https://github.com/lh3/gfatools"
       doi: "no DOI available"
-      licence: ["Unknown"]
+      licence:
+        - "Unknown"
       identifier: ""
 input:
   - - meta:
@@ -41,13 +41,27 @@ output:
           description: FASTA file
           pattern: "*.fasta"
           ontologies: []
+  versions_gfatools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - gfatools:
+          type: string
+          description: The name of the tool
+      - gfatools version | sed '1!d; s/.* //':
+          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
+      - gfatools:
+          type: string
+          description: The name of the tool
+      - gfatools version | sed '1!d; s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@mahesh-panchal"
 maintainers:

modules/nf-core/gfatools/gfa2fa/tests/main.nf.test

@@ -27,7 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -49,7 +49,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }