Update to topic phyloflash

.github/actions/nf-test-action/action.yml

@@ -58,7 +58,7 @@ runs:
       if: ${{contains(inputs.profile, 'conda')}}
       uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
-        auto-update-conda: true
+        miniconda-version: "py312_24.11.1-0"
         conda-solver: libmamba
         conda-remove-defaults: true
 

modules/nf-core/phyloflash/main.nf

@@ -4,8 +4,8 @@ process PHYLOFLASH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/phyloflash:3.4.2--hdfd78af_1' :
-        'quay.io/biocontainers/phyloflash:3.4.2--hdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d993344c3f636cb0cca9519b11fcf30faafb13fca2fd33090104e5f52d8fd643/data' :
+        'community.wave.seqera.io/library/phyloflash:3.4.2--87628969a9477d43' }"
 
     input:
     tuple val(meta), path(reads)
@@ -14,7 +14,7 @@ process PHYLOFLASH {
 
     output:
     tuple val(meta), path("${meta.id}*/*"), emit: results
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('phyloflash'), eval("phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//'"), topic: versions, emit: versions_phyloflash
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,38 +25,28 @@ process PHYLOFLASH {
     if (meta.single_end) {
         """
         phyloFlash.pl \\
-            $args \\
+            ${args} \\
             -read1 ${reads[0]} \\
-            -lib $prefix \\
+            -lib ${prefix} \\
             -interleaved \\
             -dbhome . \\
-            -CPUs $task.cpus
+            -CPUs ${task.cpus}
 
-        mkdir $prefix
-        mv ${prefix}.* $prefix
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-        END_VERSIONS
+        mkdir ${prefix}
+        mv ${prefix}.* ${prefix}
         """
     } else {
         """
         phyloFlash.pl \\
-            $args \\
+            ${args} \\
             -read1 ${reads[0]} \\
             -read2 ${reads[1]} \\
-            -lib $prefix \\
+            -lib ${prefix} \\
             -dbhome . \\
-            -CPUs $task.cpus
-
-        mkdir $prefix
-        mv ${prefix}.* $prefix
+            -CPUs ${task.cpus}
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-        END_VERSIONS
+        mkdir ${prefix}
+        mv ${prefix}.* ${prefix}
         """
     }
 
@@ -66,10 +56,5 @@ process PHYLOFLASH {
     mkdir ${prefix}
     touch ${prefix}/${prefix}.SSU.collection.fasta
     touch ${prefix}/${prefix}.phyloFlash
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-    END_VERSIONS
     """
 }

modules/nf-core/phyloflash/meta.yml

@@ -1,19 +1,18 @@
 name: phyloflash
-description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore
-  phylogenetic composition of an illumina (meta)genomic dataset.
+description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
 keywords:
   - metagenomics
   - illumina datasets
   - phylogenetic composition
 tools:
   - phyloflash:
-      description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and
-        explore phylogenetic composition of an illumina (meta)genomic dataset.
+      description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
       homepage: https://hrgv.github.io/phyloFlash/
       documentation: https://hrgv.github.io/phyloFlash/usage.html
       tool_dev_url: https://github.com/HRGV/phyloFlash
       doi: "10.1128/mSystems.00920-20"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:phyloflash
 input:
   - - meta:
@@ -44,13 +43,29 @@ output:
           type: directory
           description: Folder containing the results of phyloFlash analysis
           pattern: "${prefix}*"
+  versions_phyloflash:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - phyloflash:
+          type: string
+          description: The name of the tool
+      - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash 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
+      - phyloflash:
+          type: string
+          description: The name of the tool
+      - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@abhi18av"
 maintainers:

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

@@ -30,10 +30,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

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

@@ -2,7 +2,7 @@
     "test_phyloflash_single_end -- stub": {
         "content": [
             {
-                "0": [
+                "results": [
                     [
                         {
                             "id": "test",
@@ -14,35 +14,19 @@
                         ]
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,4880b2dc7060ad23366127e99619a2af"
-                ],
-                "results": [
+                "versions_phyloflash": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        [
-                            "test.SSU.collection.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.phyloFlash:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "PHYLOFLASH",
+                        "phyloflash",
+                        "3.4.2"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4880b2dc7060ad23366127e99619a2af"
                 ]
-            },
-            {
-                "PHYLOFLASH": {
-                    "phyloflash": "3.4.2"
-                }
             }
         ],
+        "timestamp": "2026-08-04T16:21:31.167874643",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-14T12:18:39.919595406"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }