Merge modules with new topics syntax

.pre-commit-config.yaml

@@ -4,6 +4,10 @@ repos:
     hooks:
       - id: prettier
         entry: prettier --experimental-cli --write --ignore-unknown --no-cache
+        exclude: |
+          (?x)^(
+              .*\.snap$
+          )$
         additional_dependencies:
           - [email protected]
 

modules/nf-core/bismark/align/main.nf

@@ -16,7 +16,7 @@ process BISMARK_ALIGN {
     tuple val(meta), path("*bam")       , emit: bam
     tuple val(meta), path("*report.txt"), emit: report
     tuple val(meta), path("*fq.gz")     , emit: unmapped, optional: true
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val("bismark"), eval('bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs'), topic: versions, emit: versions_bismark
 
     when:
     task.ext.when == null || task.ext.when
@@ -61,11 +61,6 @@ process BISMARK_ALIGN {
         --genome ${index} \\
         --bam \\
         ${args}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -74,10 +69,5 @@ process BISMARK_ALIGN {
     """
     touch ${prefix}.bam
     touch ${prefix}.report.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/bismark/align/meta.yml

@@ -85,13 +85,27 @@ output:
           description: Output FastQ file(s) containing unmapped reads
           pattern: "*.{fq.gz}"
           ontologies: []
+  versions_bismark:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bismark:
+          type: string
+          description: The tool name
+      - 'bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs':
+          type: string
+          description: 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
+      - bismark:
+          type: string
+          description: The tool name
+      - 'bismark --version | grep Version | sed -e "s/Bismark Version: v//" | xargs':
+          type: string
+          description: The version of the tool
 authors:
   - "@phue"
 maintainers:

modules/nf-core/bismark/align/tests/main.nf.test

@@ -53,8 +53,7 @@ nextflow_process {
                     bam(process.out.bam[0][1]).getReadsMD5(),
                     file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
                     process.out.unmapped,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -92,8 +91,7 @@ nextflow_process {
                     bam(process.out.bam[0][1]).getReadsMD5(),
                     file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
                     process.out.unmapped,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -128,8 +126,7 @@ nextflow_process {
                     bam(process.out.bam[0][1]).getReadsMD5(),
                     file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
                     process.out.unmapped,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -167,8 +164,7 @@ nextflow_process {
                     bam(process.out.bam[0][1]).getReadsMD5(),
                     file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"),
                     process.out.unmapped,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -203,8 +199,7 @@ nextflow_process {
                     bam(process.out.bam[0][1]).getReadsMD5(),
                     file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"),
                     process.out.unmapped,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )

modules/nf-core/bismark/align/tests/main.nf.test.snap

@@ -5,108 +5,113 @@
             true,
             [
 
-            ],
-            [
-                "versions.yml:md5,72777174718c419301be78c0840f1931"
             ],
             {
-                "BISMARK_ALIGN": {
-                    "bismark": "0.25.1"
-                }
+                "versions_bismark": [
+                    [
+                        "BISMARK_ALIGN",
+                        "bismark",
+                        "0.25.1"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-26T12:09:08.59445088"
+        "timestamp": "2025-10-28T15:31:46.994204006"
     },
     "hisat2 | paired-end | sarscov2 genome [fasta]": {
         "content": [
             "fb9d284aec4b2c727af3c5ffd77c6381",
             false,
             [
 
-            ],
-            [
-                "versions.yml:md5,72777174718c419301be78c0840f1931"
             ],
             {
-                "BISMARK_ALIGN": {
-                    "bismark": "0.25.1"
-                }
+                "versions_bismark": [
+                    [
+                        "BISMARK_ALIGN",
+                        "bismark",
+                        "0.25.1"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-26T12:08:47.207193467"
+        "timestamp": "2025-10-28T15:31:21.888003798"
     },
     "bowtie2 | paired-end | sarscov2 genome [fasta]": {
         "content": [
             "458c5350c3f96a8dde710985bfb62827",
             false,
             [
 
-            ],
-            [
-                "versions.yml:md5,72777174718c419301be78c0840f1931"
             ],
             {
-                "BISMARK_ALIGN": {
-                    "bismark": "0.25.1"
-                }
+                "versions_bismark": [
+                    [
+                        "BISMARK_ALIGN",
+                        "bismark",
+                        "0.25.1"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-26T12:08:02.040747075"
+        "timestamp": "2025-10-28T15:30:37.313541027"
     },
     "bowtie2 | single-end | sarscov2 genome [fasta]": {
         "content": [
             "936c0d5ce713130113e99e09a5b53afd",
             true,
             [
 
-            ],
-            [
-                "versions.yml:md5,72777174718c419301be78c0840f1931"
             ],
             {
-                "BISMARK_ALIGN": {
-                    "bismark": "0.25.1"
-                }
+                "versions_bismark": [
+                    [
+                        "BISMARK_ALIGN",
+                        "bismark",
+                        "0.25.1"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-26T12:07:37.985126432"
+        "timestamp": "2025-10-28T15:30:15.340678938"
     },
     "hisat2 | single-end | sarscov2 genome [fasta]": {
         "content": [
             "936c0d5ce713130113e99e09a5b53afd",
             true,
             [
 
-            ],
-            [
-                "versions.yml:md5,72777174718c419301be78c0840f1931"
             ],
             {
-                "BISMARK_ALIGN": {
-                    "bismark": "0.25.1"
-                }
+                "versions_bismark": [
+                    [
+                        "BISMARK_ALIGN",
+                        "bismark",
+                        "0.25.1"
+                    ]
+                ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-26T12:08:24.007957857"
+        "timestamp": "2025-10-28T15:30:58.182901875"
     }
 }

modules/nf-core/fastqc/main.nf

@@ -11,9 +11,9 @@ process FASTQC {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
+    tuple val(meta)             , path("*.html")                                                       , emit: html
+    tuple val(meta)             , path("*.zip")                                                        , emit: zip
+    tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,22 +43,12 @@ process FASTQC {
         --threads ${task.cpus} \\
         --memory ${fastqc_memory} \\
         ${renamed_files}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.html
     touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 }

modules/nf-core/fastqc/meta.yml

@@ -53,13 +53,27 @@ output:
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
           ontologies: []
+  versions_fastqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//:
+          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
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//:
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@drpatelh"
   - "@grst"