Declare deepvariant optional html output (#9469)

* Add deepvariant optional html

* update snapshot

* Update modules/nf-core/deepvariant/rundeepvariant/main.nf

Co-authored-by: Ramprasad Neethiraj <[email protected]>

* trigger html generation

* revert config change

---------

Co-authored-by: Ramprasad Neethiraj <[email protected]>

Author: peterpru

modules/nf-core/deepvariant/rundeepvariant/main.nf

@@ -20,6 +20,7 @@ process DEEPVARIANT_RUNDEEPVARIANT {
     tuple val(meta), path("${prefix}.vcf.gz.{tbi,csi}")   , emit: vcf_index
     tuple val(meta), path("${prefix}.g.vcf.gz")           , emit: gvcf
     tuple val(meta), path("${prefix}.g.vcf.gz.{tbi,csi}") , emit: gvcf_index
+    tuple val(meta), path("${prefix}.visual_report.html") , emit: report, optional: true
     path "versions.yml"                                   , emit: versions
 
     when:

modules/nf-core/deepvariant/rundeepvariant/meta.yml

@@ -122,6 +122,18 @@ output:
           description: Tabix index file of compressed GVCF
           pattern: "*.g.vcf.gz.{tbi,csi}"
           ontologies: []
+  report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.visual_report.html:
+          type: file
+          description: Visual report in HTML format
+          pattern: "*.html"
+          optional: true
+          ontologies: []
   versions:
     - versions.yml:
         type: file

modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap

@@ -39,6 +39,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -58,6 +61,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -83,10 +89,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T15:16:11.704882305"
+        "timestamp": "2025-11-28T13:05:09.499778645"
     },
     "homo_sapiens - [bam, bai] - fasta - fai": {
         "content": [
@@ -128,6 +134,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -147,6 +156,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -172,10 +184,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T15:14:44.890205274"
+        "timestamp": "2025-11-28T13:03:26.419020939"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": {
         "content": [
@@ -217,6 +229,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -236,6 +251,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -261,10 +279,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T15:15:21.933753648"
+        "timestamp": "2025-11-28T13:04:01.115384036"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": {
         "content": [
@@ -306,6 +324,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -325,6 +346,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,673ce95e6701a5e7d58ea2ab93440b27"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -350,10 +374,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-16T11:50:27.672287"
+        "timestamp": "2025-11-28T13:04:35.257314075"
     },
     "homo_sapiens - [bam, bai] - fasta - fai - stub": {
         "content": [
@@ -395,6 +419,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -414,6 +441,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -439,10 +469,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-16T11:50:55.188159"
+        "timestamp": "2025-11-28T13:05:19.534057506"
     },
     "homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai - stub": {
         "content": [
@@ -484,6 +514,9 @@
                     ]
                 ],
                 "4": [
+                    
+                ],
+                "5": [
                     "versions.yml:md5,3609b8b1430f8fa9038d70e359be0056"
                 ],
                 "gvcf": [
@@ -503,6 +536,9 @@
                         },
                         "test_out.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "report": [
+                    
                 ],
                 "vcf": [
                     [
@@ -528,9 +564,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-12T15:16:35.978912843"
+        "timestamp": "2025-11-28T13:05:29.423589845"
     }
-}
+}

modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config

@@ -1,8 +1,6 @@
 process {
-
     withName: DEEPVARIANT_RUNDEEPVARIANT {
         ext.args = params.module_args
         ext.prefix = { "${meta.id}_out" }
     }
-
 }