Multiqc2topics (#9271)

kobelavaerts · mribeirodantas · web-flow · commit e7def472e6e0 · 2025-10-29T14:36:39.000+01:00
* update multiqc to use topics for versions

* update nf-test and snapshots

* update meta.yml

* update main.nf.test after review

* removed and re-generated main.nf.test.snap after changes

* Fixing remarks

* Fix failing linting tests

---------

Co-authored-by: Marcel Ribeiro-Dantas &lt;marcel.ribeirodantas@seqera.io&gt;
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
@@ -15,10 +15,10 @@ process MULTIQC {
     path(sample_names)
 
     output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    path "*multiqc_report.html" , emit: report
+    path "*_data"               , emit: data
+    path "*_plots"              , optional:true , emit: plots
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), topic: versions, emit: versions_multiqc
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +42,6 @@ process MULTIQC {
         $replace \\
         $samples \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
@@ -55,9 +50,5 @@ process MULTIQC {
     mkdir multiqc_plots
     touch multiqc_report.html
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into
-  a single report
+description: Aggregate results from bioinformatics analyses across many samples
+  into a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -28,8 +28,8 @@ input:
         - edam: http://edamontology.org/format_3750 # YAML
   - extra_multiqc_config:
       type: file
-      description: Second optional config yml for MultiQC. Will override common sections
-        in multiqc_config.
+      description: Second optional config yml for MultiQC. Will override common
+        sections in multiqc_config.
       pattern: "*.{yml,yaml}"
       ontologies:
         - edam: http://edamontology.org/format_3750 # YAML
@@ -73,13 +73,27 @@ output:
         description: Plots created by MultiQC
         pattern: "*_data"
         ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_multiqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g:
+          type: string
+          description: The command used to generate the version of the tool
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
                 { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
             )
         }
 
@@ -56,7 +56,7 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
                 { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
             )
         }
     }
@@ -84,7 +84,7 @@ nextflow_process {
                 { assert snapshot(process.out.report.collect { file(it).getName() } +
                                 process.out.data.collect { file(it).getName() } +
                                 process.out.plots.collect { file(it).getName() } +
-                                process.out.versions ).match("multiqc_stub") }
+                                process.out.findAll { key, val -> key.startsWith("versions")} ).match() }
             )
         }
 
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,41 +1,61 @@
 {
-    "multiqc_versions_single": {
+    "sarscov2 single-end [fastqc]": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "versions_multiqc": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.32"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:33:24.356715"
+        "timestamp": "2025-10-28T15:27:59.813370216"
     },
-    "multiqc_stub": {
+    "sarscov2 single-end [fastqc] - stub": {
         "content": [
             [
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
+                {
+                    "versions_multiqc": [
+                        [
+                            "MULTIQC",
+                            "multiqc",
+                            "1.32"
+                        ]
+                    ]
+                }
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:34:11.103619"
+        "timestamp": "2025-10-28T15:30:48.963962021"
     },
-    "multiqc_versions_config": {
+    "sarscov2 single-end [fastqc] [config]": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "versions_multiqc": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.32"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:34:04.615233"
+        "timestamp": "2025-10-28T15:29:30.664969334"
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,7 @@ nextflow_process {`
`30`	`30`	`{ assert process.success },`
`31`	`31`	`{ assert process.out.report[0] ==~ ".*/multiqc_report.html" },`
`32`	`32`	`{ assert process.out.data[0] ==~ ".*/multiqc_data" },`
`33`		`- { assert snapshot(process.out.versions).match("multiqc_versions_single") }`
	`33`	`+ { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }`
`34`	`34`	`)`
`35`	`35`	`}`
`36`	`36`
`@@ -56,7 +56,7 @@ nextflow_process {`
`56`	`56`	`{ assert process.success },`
`57`	`57`	`{ assert process.out.report[0] ==~ ".*/multiqc_report.html" },`
`58`	`58`	`{ assert process.out.data[0] ==~ ".*/multiqc_data" },`
`59`		`- { assert snapshot(process.out.versions).match("multiqc_versions_config") }`
	`59`	`+ { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }`
`60`	`60`	`)`
`61`	`61`	`}`
`62`	`62`	`}`
`@@ -84,7 +84,7 @@ nextflow_process {`
`84`	`84`	`{ assert snapshot(process.out.report.collect { file(it).getName() } +`
`85`	`85`	`process.out.data.collect { file(it).getName() } +`
`86`	`86`	`process.out.plots.collect { file(it).getName() } +`
`87`		`- process.out.versions ).match("multiqc_stub") }`
	`87`	`+ process.out.findAll { key, val -> key.startsWith("versions")} ).match() }`
`88`	`88`	`)`
`89`	`89`	`}`
`90`	`90`