From d0928c7ea4ae4af287c960450befa9996e356f7a Mon Sep 17 00:00:00 2001
From: Ksenia Lavrichenko <ksenia.lavrichenko@gmail.com>
Date: Fri, 9 Oct 2026 08:40:17 +0200
Subject: [PATCH 1/2] sniffles: add forced calling (--genotype-vcf) as an
 optional input

Generated by Claude
---
 modules/nf-core/sniffles/main.nf              |   7 +-
 modules/nf-core/sniffles/meta.yml             |   8 +-
 modules/nf-core/sniffles/tests/main.nf.test   | 132 +++-
 .../nf-core/sniffles/tests/main.nf.test.snap  | 567 ++++++++++++++++++
 .../nf-core/sniffles/tests/nextflow.config    |   5 +-
 5 files changed, 707 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf
index 4dd17e660530..c3a76ad45f33 100644
--- a/modules/nf-core/sniffles/main.nf
+++ b/modules/nf-core/sniffles/main.nf
@@ -8,7 +8,7 @@ process SNIFFLES {
 :         'community.wave.seqera.io/library/sniffles:2.8.1--b8c26c44b42620c5' }"
 
     input:
-    tuple val(meta), path(input), path(index)
+    tuple val(meta), path(input), path(index), path(genotype_vcf)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(tandem_file)
     val(vcf_output)
@@ -31,13 +31,18 @@ process SNIFFLES {
     def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : ''
     def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": ''
     def snf = snf_output ? "--snf ${prefix}.snf": ''
+    // Sniffles reads the sites file as plain text, a gzipped one is decompressed first (fritzsedlazeck/Sniffles#613)
+    def decompress = genotype_vcf && genotype_vcf.name.endsWith('.gz') ? "gzip -dc ${genotype_vcf} > ${prefix}.sites.vcf" : ''
+    def genotype = genotype_vcf ? "--genotype-vcf ${genotype_vcf.name.endsWith('.gz') ? prefix + '.sites.vcf' : genotype_vcf}" : ''
 
     """
+    $decompress
     sniffles \\
         --input $input \\
         $reference \\
         -t $task.cpus \\
         $tandem_repeats \\
+        $genotype \\
         $vcf \\
         $snf \\
         $args
diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml
index c20aae086905..7d37b6988dfb 100644
--- a/modules/nf-core/sniffles/meta.yml
+++ b/modules/nf-core/sniffles/meta.yml
@@ -1,5 +1,5 @@
 name: sniffles
-description: structural-variant calling with sniffles
+description: structural-variant calling and genotyping of known structural variants (forced calling with --genotype-vcf) with sniffles. As of Sniffles 2.8.1 the genotyping output carries one more value per sample than the FORMAT declares (fritzsedlazeck/Sniffles#615).
 keywords:
   - sniffles
   - structural-variant calling
@@ -30,6 +30,12 @@ input:
         description: Index of BAM/CAM file
         pattern: "*.{bai,crai}"
         ontologies: []
+    - genotype_vcf:
+        type: file
+        description: Optional VCF of known structural variants to genotype in the input BAM/CRAM (forced calling), plain or gzipped. Use an empty list (`[]`) for regular SV calling.
+        pattern: "*.{vcf,vcf.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3016
   - - meta2:
         type: map
         description: |
diff --git a/modules/nf-core/sniffles/tests/main.nf.test b/modules/nf-core/sniffles/tests/main.nf.test
index a7f57f1a3a59..cb6d1dc601ca 100644
--- a/modules/nf-core/sniffles/tests/main.nf.test
+++ b/modules/nf-core/sniffles/tests/main.nf.test
@@ -8,6 +8,7 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "sniffles"
+    tag "gunzip"
 
     test("homo_sapiens - [bam, bai], fasta, [], true, false") {
 
@@ -17,7 +18,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -52,7 +54,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -85,7 +88,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -121,7 +125,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -162,7 +167,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -194,7 +200,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -226,7 +233,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -258,7 +266,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
                 ]
                 input[1] = [
                     [ id:'genome' ],
@@ -283,4 +292,111 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens - nanopore [bam, bai, vcf.gz], [], [], true, false - genotype") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'hg002' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz', checkIfExists: true)
+                ]
+                input[1] = [[], []]
+                input[2] = [[], []]
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    file(process.out.tbi.get(0).get(1)).name,
+                    path(process.out.vcf.get(0).get(1)).linesGzip.findAll { line -> !line.startsWith("##genotype") },
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - nanopore [bam, bai, vcf], [], [], true, false - genotype") {
+
+        setup {
+            run("GUNZIP") {
+                script "../../gunzip/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'sites' ],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id:'hg002' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai', checkIfExists: true)
+                ]).combine(GUNZIP.out.gunzip.map { _meta, vcf -> vcf })
+                input[1] = [[], []]
+                input[2] = [[], []]
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                    file(process.out.tbi.get(0).get(1)).name,
+                    path(process.out.vcf.get(0).get(1)).linesGzip.findAll { line -> !line.startsWith("##genotype") },
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - nanopore [bam, bai, vcf.gz], [], [], true, false - genotype - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'hg002' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz', checkIfExists: true)
+                ]
+                input[1] = [[], []]
+                input[2] = [[], []]
+                input[3] = true
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/sniffles/tests/main.nf.test.snap b/modules/nf-core/sniffles/tests/main.nf.test.snap
index a0651d807c66..e11c10fed216 100644
--- a/modules/nf-core/sniffles/tests/main.nf.test.snap
+++ b/modules/nf-core/sniffles/tests/main.nf.test.snap
@@ -41,6 +41,308 @@
             "nextflow": "26.04.6"
         }
     },
+    "homo_sapiens - nanopore [bam, bai, vcf.gz], [], [], true, false - genotype - stub": {
+        "content": [
+            {
+                "snf": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "hg002"
+                        },
+                        "hg002_genotyped.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "hg002"
+                        },
+                        "hg002_genotyped.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions_sniffles": [
+                    [
+                        "SNIFFLES",
+                        "sniffles",
+                        "2.8.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-10-09T06:44:34.190557113",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "homo_sapiens - nanopore [bam, bai, vcf.gz], [], [], true, false - genotype": {
+        "content": [
+            {
+                "versions_sniffles": [
+                    [
+                        "SNIFFLES",
+                        "sniffles",
+                        "2.8.1"
+                    ]
+                ]
+            },
+            "hg002_genotyped.vcf.gz.tbi",
+            [
+                "##fileformat=VCFv4.1",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the SV\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">",
+                "##contig=<ID=chr1,length=248956422>",
+                "##contig=<ID=chr2,length=242193529>",
+                "##contig=<ID=chr3,length=198295559>",
+                "##contig=<ID=chr4,length=190214555>",
+                "##contig=<ID=chr5,length=181538259>",
+                "##contig=<ID=chr6,length=170805979>",
+                "##contig=<ID=chr7,length=159345973>",
+                "##contig=<ID=chr8,length=145138636>",
+                "##contig=<ID=chr9,length=138394717>",
+                "##contig=<ID=chr10,length=133797422>",
+                "##contig=<ID=chr11,length=135086622>",
+                "##contig=<ID=chr12,length=133275309>",
+                "##contig=<ID=chr13,length=114364328>",
+                "##contig=<ID=chr14,length=107043718>",
+                "##contig=<ID=chr15,length=101991189>",
+                "##contig=<ID=chr16,length=90338345>",
+                "##contig=<ID=chr17,length=83257441>",
+                "##contig=<ID=chr18,length=80373285>",
+                "##contig=<ID=chr19,length=58617616>",
+                "##contig=<ID=chr20,length=64444167>",
+                "##contig=<ID=chr21,length=46709983>",
+                "##contig=<ID=chr22,length=50818468>",
+                "##contig=<ID=chrX,length=156040895>",
+                "##contig=<ID=chrY,length=57227415>",
+                "##contig=<ID=chr16_KI270728v1_random,length=1872759>",
+                "##contig=<ID=chrM,length=16569>",
+                "##contig=<ID=chr1_KI270706v1_random,length=175055>",
+                "##contig=<ID=chr1_KI270707v1_random,length=32032>",
+                "##contig=<ID=chr1_KI270708v1_random,length=127682>",
+                "##contig=<ID=chr1_KI270709v1_random,length=66860>",
+                "##contig=<ID=chr1_KI270710v1_random,length=40176>",
+                "##contig=<ID=chr1_KI270711v1_random,length=42210>",
+                "##contig=<ID=chr1_KI270712v1_random,length=176043>",
+                "##contig=<ID=chr1_KI270713v1_random,length=40745>",
+                "##contig=<ID=chr1_KI270714v1_random,length=41717>",
+                "##contig=<ID=chr2_KI270715v1_random,length=161471>",
+                "##contig=<ID=chr2_KI270716v1_random,length=153799>",
+                "##contig=<ID=chr3_GL000221v1_random,length=155397>",
+                "##contig=<ID=chr4_GL000008v2_random,length=209709>",
+                "##contig=<ID=chr5_GL000208v1_random,length=92689>",
+                "##contig=<ID=chr9_KI270717v1_random,length=40062>",
+                "##contig=<ID=chr9_KI270718v1_random,length=38054>",
+                "##contig=<ID=chr9_KI270719v1_random,length=176845>",
+                "##contig=<ID=chr9_KI270720v1_random,length=39050>",
+                "##contig=<ID=chr11_KI270721v1_random,length=100316>",
+                "##contig=<ID=chr14_GL000009v2_random,length=201709>",
+                "##contig=<ID=chr14_GL000225v1_random,length=211173>",
+                "##contig=<ID=chr14_KI270722v1_random,length=194050>",
+                "##contig=<ID=chr14_GL000194v1_random,length=191469>",
+                "##contig=<ID=chr14_KI270723v1_random,length=38115>",
+                "##contig=<ID=chr14_KI270724v1_random,length=39555>",
+                "##contig=<ID=chr14_KI270725v1_random,length=172810>",
+                "##contig=<ID=chr14_KI270726v1_random,length=43739>",
+                "##contig=<ID=chr15_KI270727v1_random,length=448248>",
+                "##contig=<ID=chr17_GL000205v2_random,length=185591>",
+                "##contig=<ID=chr17_KI270729v1_random,length=280839>",
+                "##contig=<ID=chr17_KI270730v1_random,length=112551>",
+                "##contig=<ID=chr22_KI270731v1_random,length=150754>",
+                "##contig=<ID=chr22_KI270732v1_random,length=41543>",
+                "##contig=<ID=chr22_KI270733v1_random,length=179772>",
+                "##contig=<ID=chr22_KI270734v1_random,length=165050>",
+                "##contig=<ID=chr22_KI270735v1_random,length=42811>",
+                "##contig=<ID=chr22_KI270736v1_random,length=181920>",
+                "##contig=<ID=chr22_KI270737v1_random,length=103838>",
+                "##contig=<ID=chr22_KI270738v1_random,length=99375>",
+                "##contig=<ID=chr22_KI270739v1_random,length=73985>",
+                "##contig=<ID=chrY_KI270740v1_random,length=37240>",
+                "##contig=<ID=chrUn_KI270302v1,length=2274>",
+                "##contig=<ID=chrUn_KI270304v1,length=2165>",
+                "##contig=<ID=chrUn_KI270303v1,length=1942>",
+                "##contig=<ID=chrUn_KI270305v1,length=1472>",
+                "##contig=<ID=chrUn_KI270322v1,length=21476>",
+                "##contig=<ID=chrUn_KI270320v1,length=4416>",
+                "##contig=<ID=chrUn_KI270310v1,length=1201>",
+                "##contig=<ID=chrUn_KI270316v1,length=1444>",
+                "##contig=<ID=chrUn_KI270315v1,length=2276>",
+                "##contig=<ID=chrUn_KI270312v1,length=998>",
+                "##contig=<ID=chrUn_KI270311v1,length=12399>",
+                "##contig=<ID=chrUn_KI270317v1,length=37690>",
+                "##contig=<ID=chrUn_KI270412v1,length=1179>",
+                "##contig=<ID=chrUn_KI270411v1,length=2646>",
+                "##contig=<ID=chrUn_KI270414v1,length=2489>",
+                "##contig=<ID=chrUn_KI270419v1,length=1029>",
+                "##contig=<ID=chrUn_KI270418v1,length=2145>",
+                "##contig=<ID=chrUn_KI270420v1,length=2321>",
+                "##contig=<ID=chrUn_KI270424v1,length=2140>",
+                "##contig=<ID=chrUn_KI270417v1,length=2043>",
+                "##contig=<ID=chrUn_KI270422v1,length=1445>",
+                "##contig=<ID=chrUn_KI270423v1,length=981>",
+                "##contig=<ID=chrUn_KI270425v1,length=1884>",
+                "##contig=<ID=chrUn_KI270429v1,length=1361>",
+                "##contig=<ID=chrUn_KI270442v1,length=392061>",
+                "##contig=<ID=chrUn_KI270466v1,length=1233>",
+                "##contig=<ID=chrUn_KI270465v1,length=1774>",
+                "##contig=<ID=chrUn_KI270467v1,length=3920>",
+                "##contig=<ID=chrUn_KI270435v1,length=92983>",
+                "##contig=<ID=chrUn_KI270438v1,length=112505>",
+                "##contig=<ID=chrUn_KI270468v1,length=4055>",
+                "##contig=<ID=chrUn_KI270510v1,length=2415>",
+                "##contig=<ID=chrUn_KI270509v1,length=2318>",
+                "##contig=<ID=chrUn_KI270518v1,length=2186>",
+                "##contig=<ID=chrUn_KI270508v1,length=1951>",
+                "##contig=<ID=chrUn_KI270516v1,length=1300>",
+                "##contig=<ID=chrUn_KI270512v1,length=22689>",
+                "##contig=<ID=chrUn_KI270519v1,length=138126>",
+                "##contig=<ID=chrUn_KI270522v1,length=5674>",
+                "##contig=<ID=chrUn_KI270511v1,length=8127>",
+                "##contig=<ID=chrUn_KI270515v1,length=6361>",
+                "##contig=<ID=chrUn_KI270507v1,length=5353>",
+                "##contig=<ID=chrUn_KI270517v1,length=3253>",
+                "##contig=<ID=chrUn_KI270529v1,length=1899>",
+                "##contig=<ID=chrUn_KI270528v1,length=2983>",
+                "##contig=<ID=chrUn_KI270530v1,length=2168>",
+                "##contig=<ID=chrUn_KI270539v1,length=993>",
+                "##contig=<ID=chrUn_KI270538v1,length=91309>",
+                "##contig=<ID=chrUn_KI270544v1,length=1202>",
+                "##contig=<ID=chrUn_KI270548v1,length=1599>",
+                "##contig=<ID=chrUn_KI270583v1,length=1400>",
+                "##contig=<ID=chrUn_KI270587v1,length=2969>",
+                "##contig=<ID=chrUn_KI270580v1,length=1553>",
+                "##contig=<ID=chrUn_KI270581v1,length=7046>",
+                "##contig=<ID=chrUn_KI270579v1,length=31033>",
+                "##contig=<ID=chrUn_KI270589v1,length=44474>",
+                "##contig=<ID=chrUn_KI270590v1,length=4685>",
+                "##contig=<ID=chrUn_KI270584v1,length=4513>",
+                "##contig=<ID=chrUn_KI270582v1,length=6504>",
+                "##contig=<ID=chrUn_KI270588v1,length=6158>",
+                "##contig=<ID=chrUn_KI270593v1,length=3041>",
+                "##contig=<ID=chrUn_KI270591v1,length=5796>",
+                "##contig=<ID=chrUn_KI270330v1,length=1652>",
+                "##contig=<ID=chrUn_KI270329v1,length=1040>",
+                "##contig=<ID=chrUn_KI270334v1,length=1368>",
+                "##contig=<ID=chrUn_KI270333v1,length=2699>",
+                "##contig=<ID=chrUn_KI270335v1,length=1048>",
+                "##contig=<ID=chrUn_KI270338v1,length=1428>",
+                "##contig=<ID=chrUn_KI270340v1,length=1428>",
+                "##contig=<ID=chrUn_KI270336v1,length=1026>",
+                "##contig=<ID=chrUn_KI270337v1,length=1121>",
+                "##contig=<ID=chrUn_KI270363v1,length=1803>",
+                "##contig=<ID=chrUn_KI270364v1,length=2855>",
+                "##contig=<ID=chrUn_KI270362v1,length=3530>",
+                "##contig=<ID=chrUn_KI270366v1,length=8320>",
+                "##contig=<ID=chrUn_KI270378v1,length=1048>",
+                "##contig=<ID=chrUn_KI270379v1,length=1045>",
+                "##contig=<ID=chrUn_KI270389v1,length=1298>",
+                "##contig=<ID=chrUn_KI270390v1,length=2387>",
+                "##contig=<ID=chrUn_KI270387v1,length=1537>",
+                "##contig=<ID=chrUn_KI270395v1,length=1143>",
+                "##contig=<ID=chrUn_KI270396v1,length=1880>",
+                "##contig=<ID=chrUn_KI270388v1,length=1216>",
+                "##contig=<ID=chrUn_KI270394v1,length=970>",
+                "##contig=<ID=chrUn_KI270386v1,length=1788>",
+                "##contig=<ID=chrUn_KI270391v1,length=1484>",
+                "##contig=<ID=chrUn_KI270383v1,length=1750>",
+                "##contig=<ID=chrUn_KI270393v1,length=1308>",
+                "##contig=<ID=chrUn_KI270384v1,length=1658>",
+                "##contig=<ID=chrUn_KI270392v1,length=971>",
+                "##contig=<ID=chrUn_KI270381v1,length=1930>",
+                "##contig=<ID=chrUn_KI270385v1,length=990>",
+                "##contig=<ID=chrUn_KI270382v1,length=4215>",
+                "##contig=<ID=chrUn_KI270376v1,length=1136>",
+                "##contig=<ID=chrUn_KI270374v1,length=2656>",
+                "##contig=<ID=chrUn_KI270372v1,length=1650>",
+                "##contig=<ID=chrUn_KI270373v1,length=1451>",
+                "##contig=<ID=chrUn_KI270375v1,length=2378>",
+                "##contig=<ID=chrUn_KI270371v1,length=2805>",
+                "##contig=<ID=chrUn_KI270448v1,length=7992>",
+                "##contig=<ID=chrUn_KI270521v1,length=7642>",
+                "##contig=<ID=chrUn_GL000195v1,length=182896>",
+                "##contig=<ID=chrUn_GL000219v1,length=179198>",
+                "##contig=<ID=chrUn_GL000220v1,length=161802>",
+                "##contig=<ID=chrUn_GL000224v1,length=179693>",
+                "##contig=<ID=chrUn_KI270741v1,length=157432>",
+                "##contig=<ID=chrUn_GL000226v1,length=15008>",
+                "##contig=<ID=chrUn_GL000213v1,length=164239>",
+                "##contig=<ID=chrUn_KI270743v1,length=210658>",
+                "##contig=<ID=chrUn_KI270744v1,length=168472>",
+                "##contig=<ID=chrUn_KI270745v1,length=41891>",
+                "##contig=<ID=chrUn_KI270746v1,length=66486>",
+                "##contig=<ID=chrUn_KI270747v1,length=198735>",
+                "##contig=<ID=chrUn_KI270748v1,length=93321>",
+                "##contig=<ID=chrUn_KI270749v1,length=158759>",
+                "##contig=<ID=chrUn_KI270750v1,length=148850>",
+                "##contig=<ID=chrUn_KI270751v1,length=150742>",
+                "##contig=<ID=chrUn_KI270752v1,length=27745>",
+                "##contig=<ID=chrUn_KI270753v1,length=62944>",
+                "##contig=<ID=chrUn_KI270754v1,length=40191>",
+                "##contig=<ID=chrUn_KI270755v1,length=36723>",
+                "##contig=<ID=chrUn_KI270756v1,length=79590>",
+                "##contig=<ID=chrUn_KI270757v1,length=71251>",
+                "##contig=<ID=chrUn_GL000214v1,length=137718>",
+                "##contig=<ID=chrUn_KI270742v1,length=186739>",
+                "##contig=<ID=chrUn_GL000216v2,length=176608>",
+                "##contig=<ID=chrUn_GL000218v1,length=161147>",
+                "##contig=<ID=chrEBV,length=171823>",
+                "##contig=<ID=MAP2K3_chr17_22578583_22605165,length=26582>",
+                "##contig=<ID=KCNJ18_chr17_22629421_22688415,length=58994>",
+                "##contig=<ID=KMT2C_chr21_7687010_7731520,length=44510>",
+                "##contig=<ID=KMT2C_chr15_6020392_6062903,length=42511>",
+                "##contig=<ID=KMT2C_chr13_14464876_14502703,length=37827>",
+                "##contig=<ID=KMT2C_chr13_14211849_14228603,length=16754>",
+                "##contig=<ID=KMT2C_chr13_10688343_10754814,length=66471>",
+                "##contig=<ID=KMT2C_chr13_10744786_10790087,length=45301>",
+                "##contig=<ID=KMT2C_chr13_11526357_11569988,length=43631>",
+                "##contig=<ID=KMT2C_chr13_11559977_11592630,length=32653>",
+                "##contig=<ID=KMT2C_chr13_14408161_14474907,length=66746>",
+                "##contig=<ID=KMT2C_chr14_3553442_3620349,length=66907>",
+                "##contig=<ID=KMT2C_chr14_3610318_3640421,length=30103>",
+                "##contig=<ID=KMT2C_chr15_5960377_6027329,length=66952>",
+                "##contig=<ID=KMT2C_chr2_89596961_89613143,length=16182>",
+                "##contig=<ID=KMT2C_chr2_90170767_90210396,length=39629>",
+                "##contig=<ID=KMT2C_chr21_7659652_7674726,length=15074>",
+                "##contig=<ID=KMT2C_chr21_8616365_8659521,length=43156>",
+                "##contig=<ID=KMT2C_chr21_8649510_8682182,length=32672>",
+                "##contig=<ID=KMT2C_chr22_6626735_6693166,length=66431>",
+                "##contig=<ID=KMT2C_chr22_6683135_6713219,length=30084>",
+                "##contig=<ID=KMT2C_chr22_11126384_11167180,length=40796>",
+                "##contig=<ID=KMT2C_chr22_11157169_11189815,length=32646>",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG002",
+                "chr2\t71691476\tSniffles2.DEL.9E7S1:HG002_sniffles_reheader|Sniffles2.DEL.9A4S1:HG003_sniffles_reheader|Sniffles2.DEL.948S1:HG004_sniffles_reheader\tTTGTCTGCTGGTGTTTTTGAGAGATTACACACACACACACACCATTTTCTGCTCCTTTTCCAGGGCTGTGTGGATAGTCCAGGATGGGGTGA\tT\t.\tPASS\tSVTYPE=DEL;SVLEN=-91;END=71691567\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr2\t71691485\tseverus_DEL5090:HG002_severus_reheader|severus_DEL4930:HG003_severus_reheader|severus_DEL4855:HG004_severus_reheader\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;SVLEN=90;END=71691575\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr2\t71691501\tDB11254:HG002_debreak_reheader|DB11408:HG003_debreak_reheader|DB11357:HG004_debreak_reheader\tN\t<DEL>\t.\tPASS\tEND=71691591;CHR2=chr2;SVLEN=91;SVTYPE=DEL\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr7\t107418983\tSniffles2.INV.BBCS6:HG002_sniffles_reheader|Sniffles2.INV.B1FS6:HG003_sniffles_reheader|Sniffles2.INV.AF3S6:HG004_sniffles_reheader:sniffles|DB20893:HG002_debreak_reheader|DB21039:HG003_debreak_reheader|DB20996:HG004_debreak_reheader:debreak|severus_INV9727:HG002_severus_reheader|severus_INV9357:HG003_severus_reheader|severus_INV9428:HG004_severus_reheader:severus\tC\t<INV>\t.\tPASS\tSVTYPE=INV;SVLEN=3349;END=107422332;CHR2=chr7\tGT:GQ:DR:DV\t1/1:9:3:14:.",
+                "chr7\t107418984\tSniffles2.BND.140DS6:HG002_sniffles_reheader|Sniffles2.BND.140FS6:HG002_sniffles_reheader|Sniffles2.BND.1952S6:HG003_sniffles_reheader|Sniffles2.BND.1954S6:HG003_sniffles_reheader|Sniffles2.BND.12EES6:HG004_sniffles_reheader|Sniffles2.BND.12F1S6:HG004_sniffles_reheader|Sniffles2.BND.12F2S6:HG004_sniffles_reheader\tA\t[chr7:107422334[A\t.\tPASS\tSVTYPE=BND;CHR2=chr7\tGT:GQ:DR:DV\t0/1:8:2:4:.",
+                "chr9\t90884156\tseverus_INS23502\tN\tATATATATATACACATACGTGTATATATATACACACATACACATACGTGTATATATACACACATACACATACGTGTATATATACACACATACACATACGTGTATATATACACGC\t.\tPASS\tSVTYPE=INS;SVLEN=112\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884250\tSniffles2.INS.2AFS8:HG002_sniffles_reheader|Sniffles2.INS.290S8:HG003_sniffles_reheader|Sniffles2.INS.27ES8:HG004_sniffles_reheader:sniffles|DB23148:HG002_debreak_reheader|DB23351:HG003_debreak_reheader|DB23301:HG004_debreak_reheader:debreak|DB23302:debreak\tC\tCATACACATACGTGTATATATACACATACACATACACATACGTGTATATATACACATACACATACACATACGTGTATATATACACACATATACACATACACATACGTGTATATATACACACATATACACATACGTGTATATATATACACATATACACATACGTGTATATATACACACAT\t.\tPASS\tSVTYPE=INS;SVLEN=178;END=90884250;CHR2=chr9\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884463\tSniffles2.INS.291S8\tG\tGTGTACATGCACATATATACACACACATATGTGTACATGCACATATATACACATACACATATGTGTACATGCACATATATACACATACACATA\t.\tPASS\tSVTYPE=INS;SVLEN=92;END=90884463\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884616\tSniffles2.INS.27FS8\tT\tTACACATATGTGTACATGTACATATATACACATACACATATGTGTACATGTACATATATACAC\t.\tPASS\tSVTYPE=INS;SVLEN=62;END=90884616\tGT:GQ:DR:DV\t0/0:34:16:1:.",
+                "chr9\t90884683\tseverus_INS23503:HG002_severus_reheader|severus_INS22991:HG003_severus_reheader\tN\tATACACATGTGTACATGCACATATATACACATACCACCCATATATAATCCACATATATATGTACATATGTGTATATATACATATATATACACATATATATGTATATATACACATATGTGAATATGTATATATGTGTATGTACATATGTGTATATGTATATATACATATATACACATATGTGTATATACACATATATACATACACATATGTCTATACATATATACATGTGCACATATGTATATATATACATATATACATATACACATGTGTATATACATATATACATATACACCTATGTGTATATATAACACATATATACATATATATATATATCACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTATATATACATATATATACATATACACATATATATATATAGACAC\t.\tPASS\tSVTYPE=INS;SVLEN=435\tGT:GQ:DR:DV\t0/1:42:10:7:.",
+                "chr9\t90884800\tDB23149:HG002_debreak_reheader|DB23352:HG003_debreak_reheader:debreak|severus_INS23123:severus\tN\t<INS>\t.\tPASS\tEND=90884800;CHR2=chr9;SVLEN=337;SVTYPE=INS\tGT:GQ:DR:DV\t0/1:54:8:9:.",
+                "chr9\t90884880\tSniffles2.INS.2B0S8:HG002_sniffles_reheader|Sniffles2.INS.293S8:HG003_sniffles_reheader|Sniffles2.INS.281S8:HG004_sniffles_reheader|Sniffles2.INS.280S8:HG004_sniffles_reheader:sniffles|DB23303:debreak\tT\tTACACATATGTGTACATATGTGTATATATACATATATATACACATATATATGTATATATACACATATGTGAATATGTATATATGTGTTATATATACACATATGTGTATATGTATATATACATATATACACATATGTGTATATACACATATATACATATACACATATGTGTATATACATATATACATATACACATATGTGTATATATACATATATACATATACACATATGTGTATATATACATATATACATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATACATATATACATATACACATATGTGTATATATA\t.\tPASS\tSVTYPE=INS;SVLEN=389;END=90884880;CHR2=chr9\tGT:GQ:DR:DV\t0/1:54:8:9:.",
+                "chr18\t57787400\tSniffles2.DEL.47ES11:HG002_sniffles_reheader|Sniffles2.DEL.448S11:HG003_sniffles_reheader|Sniffles2.DEL.47FS11:HG004_sniffles_reheader\tGCACTGCGGGAGGAGCTCCATCTAGAACACTGCGGGAGGAGCTCCATCTAGAA\tG\t.\tPASS\tSVTYPE=DEL;SVLEN=-52;END=57787452\tGT:GQ:DR:DV\t1/1:41:0:15:.",
+                "chr18\t57787402\tseverus_DEL4309:HG002_severus_reheader|severus_DEL4141:HG003_severus_reheader|severus_DEL4114:HG004_severus_reheader\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;SVLEN=53;END=57787455\tGT:GQ:DR:DV\t1/1:41:0:15:.",
+                "chr18\t57787413\tDB9486:HG002_debreak_reheader|DB9598:HG003_debreak_reheader|DB9601:HG004_debreak_reheader\tN\t<DEL>\t.\tPASS\tEND=57787463;CHR2=chr18;SVLEN=51;SVTYPE=DEL\tGT:GQ:DR:DV\t1/1:41:0:15:."
+            ]
+        ],
+        "timestamp": "2026-10-09T06:44:26.568842349",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
     "homo_sapiens - [bam, bai], fasta, [], true, false": {
         "content": [
             {
@@ -279,6 +581,271 @@
             "nextflow": "26.04.6"
         }
     },
+    "homo_sapiens - nanopore [bam, bai, vcf], [], [], true, false - genotype": {
+        "content": [
+            {
+                "versions_sniffles": [
+                    [
+                        "SNIFFLES",
+                        "sniffles",
+                        "2.8.1"
+                    ]
+                ]
+            },
+            "hg002_genotyped.vcf.gz.tbi",
+            [
+                "##fileformat=VCFv4.1",
+                "##FILTER=<ID=PASS,Description=\"All filters passed\">",
+                "##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for END\">",
+                "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the SV\">",
+                "##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of the SV\">",
+                "##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">",
+                "##contig=<ID=chr1,length=248956422>",
+                "##contig=<ID=chr2,length=242193529>",
+                "##contig=<ID=chr3,length=198295559>",
+                "##contig=<ID=chr4,length=190214555>",
+                "##contig=<ID=chr5,length=181538259>",
+                "##contig=<ID=chr6,length=170805979>",
+                "##contig=<ID=chr7,length=159345973>",
+                "##contig=<ID=chr8,length=145138636>",
+                "##contig=<ID=chr9,length=138394717>",
+                "##contig=<ID=chr10,length=133797422>",
+                "##contig=<ID=chr11,length=135086622>",
+                "##contig=<ID=chr12,length=133275309>",
+                "##contig=<ID=chr13,length=114364328>",
+                "##contig=<ID=chr14,length=107043718>",
+                "##contig=<ID=chr15,length=101991189>",
+                "##contig=<ID=chr16,length=90338345>",
+                "##contig=<ID=chr17,length=83257441>",
+                "##contig=<ID=chr18,length=80373285>",
+                "##contig=<ID=chr19,length=58617616>",
+                "##contig=<ID=chr20,length=64444167>",
+                "##contig=<ID=chr21,length=46709983>",
+                "##contig=<ID=chr22,length=50818468>",
+                "##contig=<ID=chrX,length=156040895>",
+                "##contig=<ID=chrY,length=57227415>",
+                "##contig=<ID=chr16_KI270728v1_random,length=1872759>",
+                "##contig=<ID=chrM,length=16569>",
+                "##contig=<ID=chr1_KI270706v1_random,length=175055>",
+                "##contig=<ID=chr1_KI270707v1_random,length=32032>",
+                "##contig=<ID=chr1_KI270708v1_random,length=127682>",
+                "##contig=<ID=chr1_KI270709v1_random,length=66860>",
+                "##contig=<ID=chr1_KI270710v1_random,length=40176>",
+                "##contig=<ID=chr1_KI270711v1_random,length=42210>",
+                "##contig=<ID=chr1_KI270712v1_random,length=176043>",
+                "##contig=<ID=chr1_KI270713v1_random,length=40745>",
+                "##contig=<ID=chr1_KI270714v1_random,length=41717>",
+                "##contig=<ID=chr2_KI270715v1_random,length=161471>",
+                "##contig=<ID=chr2_KI270716v1_random,length=153799>",
+                "##contig=<ID=chr3_GL000221v1_random,length=155397>",
+                "##contig=<ID=chr4_GL000008v2_random,length=209709>",
+                "##contig=<ID=chr5_GL000208v1_random,length=92689>",
+                "##contig=<ID=chr9_KI270717v1_random,length=40062>",
+                "##contig=<ID=chr9_KI270718v1_random,length=38054>",
+                "##contig=<ID=chr9_KI270719v1_random,length=176845>",
+                "##contig=<ID=chr9_KI270720v1_random,length=39050>",
+                "##contig=<ID=chr11_KI270721v1_random,length=100316>",
+                "##contig=<ID=chr14_GL000009v2_random,length=201709>",
+                "##contig=<ID=chr14_GL000225v1_random,length=211173>",
+                "##contig=<ID=chr14_KI270722v1_random,length=194050>",
+                "##contig=<ID=chr14_GL000194v1_random,length=191469>",
+                "##contig=<ID=chr14_KI270723v1_random,length=38115>",
+                "##contig=<ID=chr14_KI270724v1_random,length=39555>",
+                "##contig=<ID=chr14_KI270725v1_random,length=172810>",
+                "##contig=<ID=chr14_KI270726v1_random,length=43739>",
+                "##contig=<ID=chr15_KI270727v1_random,length=448248>",
+                "##contig=<ID=chr17_GL000205v2_random,length=185591>",
+                "##contig=<ID=chr17_KI270729v1_random,length=280839>",
+                "##contig=<ID=chr17_KI270730v1_random,length=112551>",
+                "##contig=<ID=chr22_KI270731v1_random,length=150754>",
+                "##contig=<ID=chr22_KI270732v1_random,length=41543>",
+                "##contig=<ID=chr22_KI270733v1_random,length=179772>",
+                "##contig=<ID=chr22_KI270734v1_random,length=165050>",
+                "##contig=<ID=chr22_KI270735v1_random,length=42811>",
+                "##contig=<ID=chr22_KI270736v1_random,length=181920>",
+                "##contig=<ID=chr22_KI270737v1_random,length=103838>",
+                "##contig=<ID=chr22_KI270738v1_random,length=99375>",
+                "##contig=<ID=chr22_KI270739v1_random,length=73985>",
+                "##contig=<ID=chrY_KI270740v1_random,length=37240>",
+                "##contig=<ID=chrUn_KI270302v1,length=2274>",
+                "##contig=<ID=chrUn_KI270304v1,length=2165>",
+                "##contig=<ID=chrUn_KI270303v1,length=1942>",
+                "##contig=<ID=chrUn_KI270305v1,length=1472>",
+                "##contig=<ID=chrUn_KI270322v1,length=21476>",
+                "##contig=<ID=chrUn_KI270320v1,length=4416>",
+                "##contig=<ID=chrUn_KI270310v1,length=1201>",
+                "##contig=<ID=chrUn_KI270316v1,length=1444>",
+                "##contig=<ID=chrUn_KI270315v1,length=2276>",
+                "##contig=<ID=chrUn_KI270312v1,length=998>",
+                "##contig=<ID=chrUn_KI270311v1,length=12399>",
+                "##contig=<ID=chrUn_KI270317v1,length=37690>",
+                "##contig=<ID=chrUn_KI270412v1,length=1179>",
+                "##contig=<ID=chrUn_KI270411v1,length=2646>",
+                "##contig=<ID=chrUn_KI270414v1,length=2489>",
+                "##contig=<ID=chrUn_KI270419v1,length=1029>",
+                "##contig=<ID=chrUn_KI270418v1,length=2145>",
+                "##contig=<ID=chrUn_KI270420v1,length=2321>",
+                "##contig=<ID=chrUn_KI270424v1,length=2140>",
+                "##contig=<ID=chrUn_KI270417v1,length=2043>",
+                "##contig=<ID=chrUn_KI270422v1,length=1445>",
+                "##contig=<ID=chrUn_KI270423v1,length=981>",
+                "##contig=<ID=chrUn_KI270425v1,length=1884>",
+                "##contig=<ID=chrUn_KI270429v1,length=1361>",
+                "##contig=<ID=chrUn_KI270442v1,length=392061>",
+                "##contig=<ID=chrUn_KI270466v1,length=1233>",
+                "##contig=<ID=chrUn_KI270465v1,length=1774>",
+                "##contig=<ID=chrUn_KI270467v1,length=3920>",
+                "##contig=<ID=chrUn_KI270435v1,length=92983>",
+                "##contig=<ID=chrUn_KI270438v1,length=112505>",
+                "##contig=<ID=chrUn_KI270468v1,length=4055>",
+                "##contig=<ID=chrUn_KI270510v1,length=2415>",
+                "##contig=<ID=chrUn_KI270509v1,length=2318>",
+                "##contig=<ID=chrUn_KI270518v1,length=2186>",
+                "##contig=<ID=chrUn_KI270508v1,length=1951>",
+                "##contig=<ID=chrUn_KI270516v1,length=1300>",
+                "##contig=<ID=chrUn_KI270512v1,length=22689>",
+                "##contig=<ID=chrUn_KI270519v1,length=138126>",
+                "##contig=<ID=chrUn_KI270522v1,length=5674>",
+                "##contig=<ID=chrUn_KI270511v1,length=8127>",
+                "##contig=<ID=chrUn_KI270515v1,length=6361>",
+                "##contig=<ID=chrUn_KI270507v1,length=5353>",
+                "##contig=<ID=chrUn_KI270517v1,length=3253>",
+                "##contig=<ID=chrUn_KI270529v1,length=1899>",
+                "##contig=<ID=chrUn_KI270528v1,length=2983>",
+                "##contig=<ID=chrUn_KI270530v1,length=2168>",
+                "##contig=<ID=chrUn_KI270539v1,length=993>",
+                "##contig=<ID=chrUn_KI270538v1,length=91309>",
+                "##contig=<ID=chrUn_KI270544v1,length=1202>",
+                "##contig=<ID=chrUn_KI270548v1,length=1599>",
+                "##contig=<ID=chrUn_KI270583v1,length=1400>",
+                "##contig=<ID=chrUn_KI270587v1,length=2969>",
+                "##contig=<ID=chrUn_KI270580v1,length=1553>",
+                "##contig=<ID=chrUn_KI270581v1,length=7046>",
+                "##contig=<ID=chrUn_KI270579v1,length=31033>",
+                "##contig=<ID=chrUn_KI270589v1,length=44474>",
+                "##contig=<ID=chrUn_KI270590v1,length=4685>",
+                "##contig=<ID=chrUn_KI270584v1,length=4513>",
+                "##contig=<ID=chrUn_KI270582v1,length=6504>",
+                "##contig=<ID=chrUn_KI270588v1,length=6158>",
+                "##contig=<ID=chrUn_KI270593v1,length=3041>",
+                "##contig=<ID=chrUn_KI270591v1,length=5796>",
+                "##contig=<ID=chrUn_KI270330v1,length=1652>",
+                "##contig=<ID=chrUn_KI270329v1,length=1040>",
+                "##contig=<ID=chrUn_KI270334v1,length=1368>",
+                "##contig=<ID=chrUn_KI270333v1,length=2699>",
+                "##contig=<ID=chrUn_KI270335v1,length=1048>",
+                "##contig=<ID=chrUn_KI270338v1,length=1428>",
+                "##contig=<ID=chrUn_KI270340v1,length=1428>",
+                "##contig=<ID=chrUn_KI270336v1,length=1026>",
+                "##contig=<ID=chrUn_KI270337v1,length=1121>",
+                "##contig=<ID=chrUn_KI270363v1,length=1803>",
+                "##contig=<ID=chrUn_KI270364v1,length=2855>",
+                "##contig=<ID=chrUn_KI270362v1,length=3530>",
+                "##contig=<ID=chrUn_KI270366v1,length=8320>",
+                "##contig=<ID=chrUn_KI270378v1,length=1048>",
+                "##contig=<ID=chrUn_KI270379v1,length=1045>",
+                "##contig=<ID=chrUn_KI270389v1,length=1298>",
+                "##contig=<ID=chrUn_KI270390v1,length=2387>",
+                "##contig=<ID=chrUn_KI270387v1,length=1537>",
+                "##contig=<ID=chrUn_KI270395v1,length=1143>",
+                "##contig=<ID=chrUn_KI270396v1,length=1880>",
+                "##contig=<ID=chrUn_KI270388v1,length=1216>",
+                "##contig=<ID=chrUn_KI270394v1,length=970>",
+                "##contig=<ID=chrUn_KI270386v1,length=1788>",
+                "##contig=<ID=chrUn_KI270391v1,length=1484>",
+                "##contig=<ID=chrUn_KI270383v1,length=1750>",
+                "##contig=<ID=chrUn_KI270393v1,length=1308>",
+                "##contig=<ID=chrUn_KI270384v1,length=1658>",
+                "##contig=<ID=chrUn_KI270392v1,length=971>",
+                "##contig=<ID=chrUn_KI270381v1,length=1930>",
+                "##contig=<ID=chrUn_KI270385v1,length=990>",
+                "##contig=<ID=chrUn_KI270382v1,length=4215>",
+                "##contig=<ID=chrUn_KI270376v1,length=1136>",
+                "##contig=<ID=chrUn_KI270374v1,length=2656>",
+                "##contig=<ID=chrUn_KI270372v1,length=1650>",
+                "##contig=<ID=chrUn_KI270373v1,length=1451>",
+                "##contig=<ID=chrUn_KI270375v1,length=2378>",
+                "##contig=<ID=chrUn_KI270371v1,length=2805>",
+                "##contig=<ID=chrUn_KI270448v1,length=7992>",
+                "##contig=<ID=chrUn_KI270521v1,length=7642>",
+                "##contig=<ID=chrUn_GL000195v1,length=182896>",
+                "##contig=<ID=chrUn_GL000219v1,length=179198>",
+                "##contig=<ID=chrUn_GL000220v1,length=161802>",
+                "##contig=<ID=chrUn_GL000224v1,length=179693>",
+                "##contig=<ID=chrUn_KI270741v1,length=157432>",
+                "##contig=<ID=chrUn_GL000226v1,length=15008>",
+                "##contig=<ID=chrUn_GL000213v1,length=164239>",
+                "##contig=<ID=chrUn_KI270743v1,length=210658>",
+                "##contig=<ID=chrUn_KI270744v1,length=168472>",
+                "##contig=<ID=chrUn_KI270745v1,length=41891>",
+                "##contig=<ID=chrUn_KI270746v1,length=66486>",
+                "##contig=<ID=chrUn_KI270747v1,length=198735>",
+                "##contig=<ID=chrUn_KI270748v1,length=93321>",
+                "##contig=<ID=chrUn_KI270749v1,length=158759>",
+                "##contig=<ID=chrUn_KI270750v1,length=148850>",
+                "##contig=<ID=chrUn_KI270751v1,length=150742>",
+                "##contig=<ID=chrUn_KI270752v1,length=27745>",
+                "##contig=<ID=chrUn_KI270753v1,length=62944>",
+                "##contig=<ID=chrUn_KI270754v1,length=40191>",
+                "##contig=<ID=chrUn_KI270755v1,length=36723>",
+                "##contig=<ID=chrUn_KI270756v1,length=79590>",
+                "##contig=<ID=chrUn_KI270757v1,length=71251>",
+                "##contig=<ID=chrUn_GL000214v1,length=137718>",
+                "##contig=<ID=chrUn_KI270742v1,length=186739>",
+                "##contig=<ID=chrUn_GL000216v2,length=176608>",
+                "##contig=<ID=chrUn_GL000218v1,length=161147>",
+                "##contig=<ID=chrEBV,length=171823>",
+                "##contig=<ID=MAP2K3_chr17_22578583_22605165,length=26582>",
+                "##contig=<ID=KCNJ18_chr17_22629421_22688415,length=58994>",
+                "##contig=<ID=KMT2C_chr21_7687010_7731520,length=44510>",
+                "##contig=<ID=KMT2C_chr15_6020392_6062903,length=42511>",
+                "##contig=<ID=KMT2C_chr13_14464876_14502703,length=37827>",
+                "##contig=<ID=KMT2C_chr13_14211849_14228603,length=16754>",
+                "##contig=<ID=KMT2C_chr13_10688343_10754814,length=66471>",
+                "##contig=<ID=KMT2C_chr13_10744786_10790087,length=45301>",
+                "##contig=<ID=KMT2C_chr13_11526357_11569988,length=43631>",
+                "##contig=<ID=KMT2C_chr13_11559977_11592630,length=32653>",
+                "##contig=<ID=KMT2C_chr13_14408161_14474907,length=66746>",
+                "##contig=<ID=KMT2C_chr14_3553442_3620349,length=66907>",
+                "##contig=<ID=KMT2C_chr14_3610318_3640421,length=30103>",
+                "##contig=<ID=KMT2C_chr15_5960377_6027329,length=66952>",
+                "##contig=<ID=KMT2C_chr2_89596961_89613143,length=16182>",
+                "##contig=<ID=KMT2C_chr2_90170767_90210396,length=39629>",
+                "##contig=<ID=KMT2C_chr21_7659652_7674726,length=15074>",
+                "##contig=<ID=KMT2C_chr21_8616365_8659521,length=43156>",
+                "##contig=<ID=KMT2C_chr21_8649510_8682182,length=32672>",
+                "##contig=<ID=KMT2C_chr22_6626735_6693166,length=66431>",
+                "##contig=<ID=KMT2C_chr22_6683135_6713219,length=30084>",
+                "##contig=<ID=KMT2C_chr22_11126384_11167180,length=40796>",
+                "##contig=<ID=KMT2C_chr22_11157169_11189815,length=32646>",
+                "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
+                "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype quality\">",
+                "##FORMAT=<ID=DR,Number=1,Type=Integer,Description=\"Number of reference reads\">",
+                "##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of variant reads\">",
+                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG002",
+                "chr2\t71691476\tSniffles2.DEL.9E7S1:HG002_sniffles_reheader|Sniffles2.DEL.9A4S1:HG003_sniffles_reheader|Sniffles2.DEL.948S1:HG004_sniffles_reheader\tTTGTCTGCTGGTGTTTTTGAGAGATTACACACACACACACACCATTTTCTGCTCCTTTTCCAGGGCTGTGTGGATAGTCCAGGATGGGGTGA\tT\t.\tPASS\tSVTYPE=DEL;SVLEN=-91;END=71691567\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr2\t71691485\tseverus_DEL5090:HG002_severus_reheader|severus_DEL4930:HG003_severus_reheader|severus_DEL4855:HG004_severus_reheader\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;SVLEN=90;END=71691575\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr2\t71691501\tDB11254:HG002_debreak_reheader|DB11408:HG003_debreak_reheader|DB11357:HG004_debreak_reheader\tN\t<DEL>\t.\tPASS\tEND=71691591;CHR2=chr2;SVLEN=91;SVTYPE=DEL\tGT:GQ:DR:DV\t0/1:57:8:8:.",
+                "chr7\t107418983\tSniffles2.INV.BBCS6:HG002_sniffles_reheader|Sniffles2.INV.B1FS6:HG003_sniffles_reheader|Sniffles2.INV.AF3S6:HG004_sniffles_reheader:sniffles|DB20893:HG002_debreak_reheader|DB21039:HG003_debreak_reheader|DB20996:HG004_debreak_reheader:debreak|severus_INV9727:HG002_severus_reheader|severus_INV9357:HG003_severus_reheader|severus_INV9428:HG004_severus_reheader:severus\tC\t<INV>\t.\tPASS\tSVTYPE=INV;SVLEN=3349;END=107422332;CHR2=chr7\tGT:GQ:DR:DV\t1/1:9:3:14:.",
+                "chr7\t107418984\tSniffles2.BND.140DS6:HG002_sniffles_reheader|Sniffles2.BND.140FS6:HG002_sniffles_reheader|Sniffles2.BND.1952S6:HG003_sniffles_reheader|Sniffles2.BND.1954S6:HG003_sniffles_reheader|Sniffles2.BND.12EES6:HG004_sniffles_reheader|Sniffles2.BND.12F1S6:HG004_sniffles_reheader|Sniffles2.BND.12F2S6:HG004_sniffles_reheader\tA\t[chr7:107422334[A\t.\tPASS\tSVTYPE=BND;CHR2=chr7\tGT:GQ:DR:DV\t0/1:8:2:4:.",
+                "chr9\t90884156\tseverus_INS23502\tN\tATATATATATACACATACGTGTATATATATACACACATACACATACGTGTATATATACACACATACACATACGTGTATATATACACACATACACATACGTGTATATATACACGC\t.\tPASS\tSVTYPE=INS;SVLEN=112\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884250\tSniffles2.INS.2AFS8:HG002_sniffles_reheader|Sniffles2.INS.290S8:HG003_sniffles_reheader|Sniffles2.INS.27ES8:HG004_sniffles_reheader:sniffles|DB23148:HG002_debreak_reheader|DB23351:HG003_debreak_reheader|DB23301:HG004_debreak_reheader:debreak|DB23302:debreak\tC\tCATACACATACGTGTATATATACACATACACATACACATACGTGTATATATACACATACACATACACATACGTGTATATATACACACATATACACATACACATACGTGTATATATACACACATATACACATACGTGTATATATATACACATATACACATACGTGTATATATACACACAT\t.\tPASS\tSVTYPE=INS;SVLEN=178;END=90884250;CHR2=chr9\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884463\tSniffles2.INS.291S8\tG\tGTGTACATGCACATATATACACACACATATGTGTACATGCACATATATACACATACACATATGTGTACATGCACATATATACACATACACATA\t.\tPASS\tSVTYPE=INS;SVLEN=92;END=90884463\tGT:GQ:DR:DV\t1/1:47:0:17:.",
+                "chr9\t90884616\tSniffles2.INS.27FS8\tT\tTACACATATGTGTACATGTACATATATACACATACACATATGTGTACATGTACATATATACAC\t.\tPASS\tSVTYPE=INS;SVLEN=62;END=90884616\tGT:GQ:DR:DV\t0/0:34:16:1:.",
+                "chr9\t90884683\tseverus_INS23503:HG002_severus_reheader|severus_INS22991:HG003_severus_reheader\tN\tATACACATGTGTACATGCACATATATACACATACCACCCATATATAATCCACATATATATGTACATATGTGTATATATACATATATATACACATATATATGTATATATACACATATGTGAATATGTATATATGTGTATGTACATATGTGTATATGTATATATACATATATACACATATGTGTATATACACATATATACATACACATATGTCTATACATATATACATGTGCACATATGTATATATATACATATATACATATACACATGTGTATATACATATATACATATACACCTATGTGTATATATAACACATATATACATATATATATATATCACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTATATATACATATATATACATATACACATATATATATATAGACAC\t.\tPASS\tSVTYPE=INS;SVLEN=435\tGT:GQ:DR:DV\t0/1:42:10:7:.",
+                "chr9\t90884800\tDB23149:HG002_debreak_reheader|DB23352:HG003_debreak_reheader:debreak|severus_INS23123:severus\tN\t<INS>\t.\tPASS\tEND=90884800;CHR2=chr9;SVLEN=337;SVTYPE=INS\tGT:GQ:DR:DV\t0/1:54:8:9:.",
+                "chr9\t90884880\tSniffles2.INS.2B0S8:HG002_sniffles_reheader|Sniffles2.INS.293S8:HG003_sniffles_reheader|Sniffles2.INS.281S8:HG004_sniffles_reheader|Sniffles2.INS.280S8:HG004_sniffles_reheader:sniffles|DB23303:debreak\tT\tTACACATATGTGTACATATGTGTATATATACATATATATACACATATATATGTATATATACACATATGTGAATATGTATATATGTGTTATATATACACATATGTGTATATGTATATATACATATATACACATATGTGTATATACACATATATACATATACACATATGTGTATATACATATATACATATACACATATGTGTATATATACATATATACATATACACATATGTGTATATATACATATATACATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATAACACATATATACACCTATGTGTATATATACATATATACATATACACATATGTGTATATATA\t.\tPASS\tSVTYPE=INS;SVLEN=389;END=90884880;CHR2=chr9\tGT:GQ:DR:DV\t0/1:54:8:9:.",
+                "chr18\t57787400\tSniffles2.DEL.47ES11:HG002_sniffles_reheader|Sniffles2.DEL.448S11:HG003_sniffles_reheader|Sniffles2.DEL.47FS11:HG004_sniffles_reheader\tGCACTGCGGGAGGAGCTCCATCTAGAACACTGCGGGAGGAGCTCCATCTAGAA\tG\t.\tPASS\tSVTYPE=DEL;SVLEN=-52;END=57787452\tGT:GQ:DR:DV\t1/1:41:0:15:.",
+                "chr18\t57787402\tseverus_DEL4309:HG002_severus_reheader|severus_DEL4141:HG003_severus_reheader|severus_DEL4114:HG004_severus_reheader\tN\t<DEL>\t.\tPASS\tSVTYPE=DEL;SVLEN=53;END=57787455\tGT:GQ:DR:DV\t1/1:41:0:15:.",
+                "chr18\t57787413\tDB9486:HG002_debreak_reheader|DB9598:HG003_debreak_reheader|DB9601:HG004_debreak_reheader\tN\t<DEL>\t.\tPASS\tEND=57787463;CHR2=chr18;SVLEN=51;SVTYPE=DEL\tGT:GQ:DR:DV\t1/1:41:0:15:."
+            ]
+        ],
+        "timestamp": "2026-10-09T06:46:04.541702127",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
     "homo_sapiens - [bam, bai], fasta, [], true, true -stub": {
         "content": [
             {
diff --git a/modules/nf-core/sniffles/tests/nextflow.config b/modules/nf-core/sniffles/tests/nextflow.config
index 06e383629653..3b867134c29c 100644
--- a/modules/nf-core/sniffles/tests/nextflow.config
+++ b/modules/nf-core/sniffles/tests/nextflow.config
@@ -1,5 +1,6 @@
 process {
     withName: 'SNIFFLES' {
-        ext.args = '--minsupport 1 --no-qc --mapq 0'
-        }
+        ext.args = { genotype_vcf ? '' : '--minsupport 1 --no-qc --mapq 0' }
+        ext.prefix = { genotype_vcf ? "${meta.id}_genotyped" : meta.id }
+    }
 }

From c0d4b44eb35202d9ef8b2e0246448314c69f48dd Mon Sep 17 00:00:00 2001
From: Ksenia Lavrichenko <ksenia.lavrichenko@gmail.com>
Date: Fri, 9 Oct 2026 10:40:02 +0200
Subject: [PATCH 2/2] sniffles: remove the Sniffles#615 note from the meta.yml
 description

Generated by Claude
---
 modules/nf-core/sniffles/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml
index 7d37b6988dfb..f580a3528fcf 100644
--- a/modules/nf-core/sniffles/meta.yml
+++ b/modules/nf-core/sniffles/meta.yml
@@ -1,5 +1,5 @@
 name: sniffles
-description: structural-variant calling and genotyping of known structural variants (forced calling with --genotype-vcf) with sniffles. As of Sniffles 2.8.1 the genotyping output carries one more value per sample than the FORMAT declares (fritzsedlazeck/Sniffles#615).
+description: structural-variant calling and genotyping of known structural variants (forced calling with --genotype-vcf) with sniffles.
 keywords:
   - sniffles
   - structural-variant calling