diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf index 33da4675ed1c..d7f2a1d41b97 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/main.nf +++ b/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: diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml index 2c3ba0ad4142..6adc22b7c7e9 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/meta.yml +++ b/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 diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap index 25300a06934a..673c7013c23e 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap +++ b/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" } -} +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config index 161183de4a4d..9693059b83d5 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config +++ b/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" } } - }