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 1/4] 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 2/4] 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

From 7503a944604259b170d8899ef1acf502db3c2656 Mon Sep 17 00:00:00 2001
From: Ksenia Lavrichenko <ksenia.lavrichenko@gmail.com>
Date: Tue, 13 Oct 2026 09:15:07 +0200
Subject: [PATCH 3/4] sniffles: add htslib to the environment and rebuild the
 containers

Provides bgzip in the container.
---
 ... => linux_amd64-bd-14a95caca8d8452b_1.txt} | 142 ++++++++++--------
 ... => linux_arm64-bd-0caddb2114424a6f_1.txt} | 105 +++++++------
 modules/nf-core/sniffles/environment.yml      |   1 +
 modules/nf-core/sniffles/main.nf              |   4 +-
 modules/nf-core/sniffles/meta.yml             |  30 ++--
 5 files changed, 159 insertions(+), 123 deletions(-)
 rename modules/nf-core/sniffles/.conda-lock/{linux_amd64-bd-b8c26c44b42620c5_1.txt => linux_amd64-bd-14a95caca8d8452b_1.txt} (89%)
 rename modules/nf-core/sniffles/.conda-lock/{linux_arm64-bd-db3310e27781522c_1.txt => linux_arm64-bd-0caddb2114424a6f_1.txt} (90%)

diff --git a/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-b8c26c44b42620c5_1.txt b/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-14a95caca8d8452b_1.txt
similarity index 89%
rename from modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-b8c26c44b42620c5_1.txt
rename to modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-14a95caca8d8452b_1.txt
index cc0e54d6ad49..f155b083e650 100644
--- a/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-b8c26c44b42620c5_1.txt
+++ b/modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-14a95caca8d8452b_1.txt
@@ -14,15 +14,16 @@ linux-64:
 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_10.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.8-hebe6cf0_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/htslib-1.24-ha79157c_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-py310h44b86e0_2.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-h7cc23a3_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-hbc21106_2.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_103.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-11_h4a7cf45_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-11_h0358290_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.22.0-ha042cf0_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-hd45a770_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h373387f_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.26-h351257e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20260512-pl5321h373387f_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h280c20c_3.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.5-hd2095e1_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.7.0-h81df57d_1.conda
@@ -36,20 +37,20 @@ linux-64:
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h74cf4be_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.34-pthreads_hf13c14d_2.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libpsl-0.23.1-hd9e3e90_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libpython-3.13.15-hdc7f604_103_cp313.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.4-h0737f62_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libpython-3.13.16-hdc7f604_101_cp313.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.54.0-h13e7031_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-h6154650_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-16.2.0-h934c35e_7.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.4-hcfc3c73_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_3.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.3-py313hb5f73ae_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.4-py313hb5f73ae_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.5-h781a0a9_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/psutil-7.2.2-py313hd42f317_3.conda
-- conda: https://conda.anaconda.org/bioconda/linux-64/pysam-0.24.1-py313h4b224ce_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-64/pysam-0.24.0-py313h4b224ce_1.conda
 - conda: https://conda.anaconda.org/bioconda/linux-64/pyspoa-0.3.2-py313h7fbb527_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.15-hf47f18c_103_cp313.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.16-hf47f18c_101_cp313.conda
 - conda: https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.9.post1-py313hcd54142_3.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-9_cp313.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-hd6e31c0_1.conda
@@ -100,6 +101,22 @@ depends:
 license: ISC
 size: 131780
 timestamp: 1784754889428
+- conda: https://conda.anaconda.org/bioconda/linux-64/htslib-1.24-ha79157c_0.conda
+sha256: 97e0f0b8700f56b1ade3034f81070ede705fce3ef9a1b5f15e79e3eb9997ac17
+md5: 232775112c6fea38e9e7c25d2a58d7d2
+depends:
+- __glibc >=2.17,<3.0.a0
+- bzip2 >=1.0.8,<2.0a0
+- libcurl >=8.21.0,<9.0a0
+- libdeflate >=1.25,<1.27.0a0
+- libgcc >=14
+- liblzma >=5.8.3,<6.0a0
+- libzlib >=1.3.2,<2.0a0
+- openssl >=3.5.7,<4.0a0
+license: MIT
+license_family: MIT
+size: 1166222
+timestamp: 1783611817902
 - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-py310h44b86e0_2.conda
 sha256: 9f07834f0c546ab14d885ce0366285f61f44e326c0edd1fc63b8294e113ae432
 md5: 72a381cbad04f24b1c2a43ef707f45b4
@@ -135,9 +152,9 @@ license: MIT
 license_family: MIT
 size: 1394333
 timestamp: 1786762112514
-- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_102.conda
-sha256: 27d83f1188cd19bcb7754a078b3fa7f4cfb8527f8eb2fde54dd01fc529d1adec
-md5: 449500f2c089da11c40f5c21312e3e07
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_103.conda
+sha256: 901649b1edbe841fd4ee7e2d491a05184ed540eb01cdae506872f344babc1d28
+md5: 2362c70e7e79827c32db35547d9c179b
 depends:
 - __glibc >=2.17,<3.0.a0
 - zstd >=1.5.7,<1.6.0a0
@@ -145,8 +162,8 @@ constrains:
 - binutils_impl_linux-64 2.46.1
 license: GPL-3.0-only
 license_family: GPL
-size: 745303
-timestamp: 1784214507189
+size: 742109
+timestamp: 1791565468810
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-11_h4a7cf45_openblas.conda
 build_number: 11
 sha256: d942e0c820d60a613a6f786d074f0820fb6343e3f1ccfb110b1d98b44fb75968
@@ -195,28 +212,28 @@ license: curl
 license_family: MIT
 size: 499651
 timestamp: 1788340719230
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-hd45a770_1.conda
-sha256: 82e134c8a08b1eed9a2ed8ab578b89aa1730dcde3dea8dd87645ed0637878e54
-md5: 40f9b31aa9cf007789867df0decd0492
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.26-h351257e_0.conda
+sha256: f437f68abb1fa1dededd082a0c2800bec40495e01cf9ec46f4e693e34d60b644
+md5: d0c17fc12939a990f0865b7a14b49cfe
 depends:
 - __glibc >=2.17,<3.0.a0
-- libgcc >=14
+- libgcc >=15
 license: MIT
 license_family: MIT
-size: 73710
-timestamp: 1785908694612
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h373387f_1.conda
-sha256: 6473eb8caf2aae830f37caa93db9b26dddf7ac84b63229e8bf7fc0e5c3ab95b0
-md5: 50708d3b951d0f8e2d7f2df5b5edc040
+size: 74338
+timestamp: 1787442593524
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20260512-pl5321h373387f_0.conda
+sha256: 45301f14f4eb66da57cfaf2d265f3eeee73f8b07e99614ee3afc5b26eea91126
+md5: 27dbd7e2984b8fe48e069379636ccfdd
 depends:
 - ncurses
-- libgcc >=14
 - __glibc >=2.17,<3.0.a0
+- libgcc >=14
 - ncurses >=6.6,<7.0a0
 license: BSD-2-Clause
 license_family: BSD
-size: 135098
-timestamp: 1786616658086
+size: 135877
+timestamp: 1791327370514
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h280c20c_3.conda
 sha256: e4418f68d01a6307c4431b585c71b584f40189877364e542ee87deb777f5e85b
 md5: 7bc31538d6e3fb349e897353969237ec
@@ -371,27 +388,28 @@ license: MIT
 license_family: MIT
 size: 72519
 timestamp: 1786970753847
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libpython-3.13.15-hdc7f604_103_cp313.conda
-build_number: 103
-sha256: a25db25aad6cbf53e523e1f310713f31372932d5db655f1f2d62a204c7cdf1d7
-md5: e64cd43bbd07afafbc458138e979c851
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libpython-3.13.16-hdc7f604_101_cp313.conda
+build_number: 101
+sha256: 7a01347dfc0d99c6592010fc278500ab12fc852d902f35beca69608c5f1282d5
+md5: 6c9b3aaaa24997d37c5e193cfdca3938
 depends:
 - __glibc >=2.17,<3.0.a0
 - libgcc >=15
 - libstdcxx >=15
 license: Python-2.0
-size: 9711017
-timestamp: 1788387797958
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.4-h0737f62_102.conda
-sha256: 0f6e60634de2b55da15772fe65485965fd9b61afcce0d749c1446f625babba30
-md5: 59ec6dc9fa87a6687c00969d4dcfcd97
+size: 9718885
+timestamp: 1791334276485
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.54.0-h13e7031_1.conda
+sha256: 4823e42fe95fc318d7af6125dc6ef33bd60c1152054d41661413250dc0e84e6c
+md5: bb145547395d3329f3a1d930de9848b2
 depends:
 - __glibc >=2.17,<3.0.a0
+- icu >=78.3,<79.0a0
 - libgcc >=15
 - libzlib >=1.3.2,<2.0a0
 license: blessing
-size: 969522
-timestamp: 1791167270446
+size: 984364
+timestamp: 1791584378129
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-h6154650_1.conda
 sha256: 7e463000fa1cba3f3a6597b776f6ab301d425a96e3bc20d0d9d76a3b9f237aa3
 md5: 5c526561e1d2a2e071941174eae84557
@@ -446,24 +464,24 @@ depends:
 license: X11 AND BSD-3-Clause
 size: 911196
 timestamp: 1786355078102
-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.3-py313hb5f73ae_0.conda
-sha256: 7093b2633416f91147ed92583b7af6454d9349805601c5bbac8cef2d31f955c6
-md5: efea38e4c681d5c33aade39330bea01c
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.5.4-py313hb5f73ae_0.conda
+sha256: e8ffae51383b57192b018bdeeb95c84ec617aa1428656825b1d4a326b81410dd
+md5: 1ddee4b1dc2f784b4137a43789be3816
 depends:
 - python
+- libstdcxx >=15
 - libgcc >=15
 - __glibc >=2.17,<3.0.a0
-- libstdcxx >=15
-- liblapack >=3.9.0,<4.0a0
-- python_abi 3.13.* *_cp313
 - libcblas >=3.9.0,<4.0a0
 - libblas >=3.9.0,<4.0a0
+- liblapack >=3.9.0,<4.0a0
+- python_abi 3.13.* *_cp313
 constrains:
 - numpy-base <0a0
 license: BSD-3-Clause
 license_family: BSD
-size: 9327632
-timestamp: 1788731990928
+size: 9339599
+timestamp: 1791675323834
 - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.5-h781a0a9_0.conda
 sha256: 9c1533f1cf784f0e250919c0c9762d0b0e6bc727a79290ffb7cea1ceca1d038c
 md5: 5a51a2ea653f120240b1a9bf76e0aae9
@@ -498,23 +516,23 @@ license: BSD-3-Clause
 license_family: BSD
 size: 228778
 timestamp: 1789682033076
-- conda: https://conda.anaconda.org/bioconda/linux-64/pysam-0.24.1-py313h4b224ce_0.conda
-sha256: eb73a4489d05f90ba9201b9e513de23debd0a469e4329d15d673dc8fa3bb3ec6
-md5: b5066e4bb25e67bb7d0f1fcfda9bf473
+- conda: https://conda.anaconda.org/bioconda/linux-64/pysam-0.24.0-py313h4b224ce_1.conda
+sha256: b403d9bd3e323059947f46b49f8fd089c9ef3f8fc0e7ae289a0300510945d48b
+md5: e4c65716cd3a0396374338903f76ca18
 depends:
 - __glibc >=2.17,<3.0.a0
 - bzip2 >=1.0.8,<2.0a0
-- libcurl >=8.22.0,<9.0a0
-- libdeflate >=1.25,<1.26.0a0
+- libcurl >=8.20.0,<9.0a0
+- libdeflate >=1.25,<1.27.0a0
 - libgcc >=14
 - liblzma >=5.8.3,<6.0a0
 - libzlib >=1.3.2,<2.0a0
-- openssl >=3.5.8,<4.0a0
+- openssl >=3.5.7,<4.0a0
 - python >=3.13,<3.14.0a0
 - python_abi 3.13.* *_cp313
 license: MIT
-size: 2416044
-timestamp: 1788774307031
+size: 3834397
+timestamp: 1781872972695
 - conda: https://conda.anaconda.org/bioconda/linux-64/pyspoa-0.3.2-py313h7fbb527_1.conda
 sha256: aff751dddf410cd725de3835d7f930c2e32723526df9c09fd2cf2d1b0ce6d813
 md5: 8705f2aa9de91101864c9b24ad950125
@@ -528,32 +546,32 @@ license: MIT
 license_family: MIT
 size: 146607
 timestamp: 1772013275814
-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.15-hf47f18c_103_cp313.conda
-build_number: 103
-sha256: cc18ba39af0d591ac012c1334ac98aa59ec7be389719b4cd80cc0a58a53019de
-md5: 641613f2d89da811bc29fa4cde88ef20
+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.16-hf47f18c_101_cp313.conda
+build_number: 101
+sha256: 914ce0022ee08951329ce85d8a35f55fa11e74239568bca6102375d630ca9e61
+md5: 85450b9eb16e2b58d2cae71600e6fbde
 depends:
 - __glibc >=2.17,<3.0.a0
 - bzip2 >=1.0.8,<2.0a0
 - ld_impl_linux-64 >=2.36.1
-- libexpat >=2.8.1,<3.0a0
+- libexpat >=2.8.5,<3.0a0
 - libffi >=3.7.0,<3.8.0a0
 - libgcc >=15
 - liblzma >=5.8.3,<6.0a0
 - libmpdec >=4.0.0,<5.0a0
-- libpython 3.13.15 hdc7f604_103_cp313
+- libpython 3.13.16 hdc7f604_101_cp313
 - libsqlite >=3.53.4,<4.0a0
-- libuuid >=2.42.3,<3.0a0
+- libuuid >=2.42.4,<3.0a0
 - libzlib >=1.3.2,<2.0a0
 - ncurses >=6.6,<7.0a0
-- openssl >=3.5.8,<4.0a0
+- openssl >=3.5.9,<4.0a0
 - python_abi 3.13.* *_cp313
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
 license: Python-2.0
-size: 24369771
-timestamp: 1788387840141
+size: 24430407
+timestamp: 1791334320130
 python_site_packages_path: lib/python3.13/site-packages
 - conda: https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.9.post1-py313hcd54142_3.conda
 sha256: 923be61f592f597f4437ee77550a8e9e76d45b2bdefca919939652cd05175c5f
diff --git a/modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-db3310e27781522c_1.txt b/modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-0caddb2114424a6f_1.txt
similarity index 90%
rename from modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-db3310e27781522c_1.txt
rename to modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-0caddb2114424a6f_1.txt
index 5163d12a79d4..5d8796eda51e 100644
--- a/modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-db3310e27781522c_1.txt
+++ b/modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-0caddb2114424a6f_1.txt
@@ -14,15 +14,16 @@ linux-aarch64:
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_10.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/c-ares-1.34.8-h29ee22c_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/bioconda/linux-aarch64/htslib-1.24-h190289e_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/icu-78.3-py311h3512406_2.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/keyutils-1.6.3-h5bc82ec_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.22.2-h095d8e5_2.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.46.1-default_h1979696_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.46.1-default_h1979696_103.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-11_haddc8a3_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-11_hd72aa62_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libcurl-8.22.0-h86273da_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-hfa851ae_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libedit-3.1.20250104-pl5321hc48eb74_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libedit-3.1.20260512-pl5321hc48eb74_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libev-4.33-h80f16a2_3.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.8.5-h4154aff_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.7.0-hdaad0be_1.conda
@@ -36,20 +37,20 @@ linux-aarch64:
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libnghttp2-1.68.1-ha4b982d_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libopenblas-0.3.34-pthreads_h4148b7d_2.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpsl-0.23.1-hb8431ed_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpython-3.13.15-hc71fabe_103_cp313.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.4-hd26f1b6_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpython-3.13.16-hc71fabe_101_cp313.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.54.0-h399dd60_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libssh2-1.11.1-h7572e3e_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libstdcxx-16.2.0-hef695bb_7.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libuuid-2.42.4-hd6fdeab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_3.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-h2b6f883_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.5.3-py313h6bbad23_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.5.4-py313h6bbad23_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.5-he6ad1d5_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/psutil-7.2.2-py313he745173_3.conda
 - conda: https://conda.anaconda.org/bioconda/linux-aarch64/pysam-0.24.1-py313h24b3ded_0.conda
 - conda: https://conda.anaconda.org/bioconda/linux-aarch64/pyspoa-0.3.2-py313h30571f8_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.13.15-hd0fdf85_103_cp313.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.13.16-hd0fdf85_101_cp313.conda
 - conda: https://conda.anaconda.org/bioconda/linux-aarch64/python-edlib-1.3.9.post1-py313haca9121_3.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-9_cp313.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/readline-8.3-ha7194a6_1.conda
@@ -97,6 +98,21 @@ depends:
 license: ISC
 size: 131780
 timestamp: 1784754889428
+- conda: https://conda.anaconda.org/bioconda/linux-aarch64/htslib-1.24-h190289e_0.conda
+sha256: 47c8da1a9ce9b869317cc10e21a398ec06ff7c70c4d3225adada9b80cf545763
+md5: ea768dafa6258f2945f67dc1861543e5
+depends:
+- bzip2 >=1.0.8,<2.0a0
+- libcurl >=8.21.0,<9.0a0
+- libdeflate >=1.25,<1.26.0a0
+- libgcc >=14
+- liblzma >=5.8.3,<6.0a0
+- libzlib >=1.3.2,<2.0a0
+- openssl >=3.5.7,<4.0a0
+license: MIT
+license_family: MIT
+size: 1365711
+timestamp: 1783611529314
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/icu-78.3-py311h3512406_2.conda
 sha256: 54d921defd947adb58a90e10203d3bfe6c1f209f5f1a1ad2c6a9f7617f2fb59e
 md5: b35bbb1b957440ed742f35fb96eb7f1c
@@ -129,17 +145,17 @@ license: MIT
 license_family: MIT
 size: 1538590
 timestamp: 1786762058856
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.46.1-default_h1979696_102.conda
-sha256: 2c4901f4227b0850328ed0c69f958b30ad2cd18982f7a31c7c1f911827004d08
-md5: 489444d0acb2a579d2a002d85a08c059
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.46.1-default_h1979696_103.conda
+sha256: 516808982ad26ebdc4a9d8f71ee86ea55d0bc95382b7bca80620e0ac220971f3
+md5: ca781d8b499c39ddfe10e55a0347d6d9
 depends:
 - zstd >=1.5.7,<1.6.0a0
 constrains:
 - binutils_impl_linux-aarch64 2.46.1
 license: GPL-3.0-only
 license_family: GPL
-size: 905305
-timestamp: 1784214534868
+size: 905349
+timestamp: 1791565559147
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-11_haddc8a3_openblas.conda
 build_number: 11
 sha256: c15ae151597be9b1b1ebc6519288a1849269ae0a6315205d4a6a1186df1a936b
@@ -196,17 +212,17 @@ license: MIT
 license_family: MIT
 size: 71628
 timestamp: 1785908730449
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libedit-3.1.20250104-pl5321hc48eb74_1.conda
-sha256: 2d7218da06f1121619335bff25a2669df810dee90d2eb65b17f8b2e6b1c0d372
-md5: 6e06eb2c9fda76721699bcdd759b9c60
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libedit-3.1.20260512-pl5321hc48eb74_0.conda
+sha256: 58fd637d0219016bb69edf2973b089975de283e8a38149d69ef586b8fc4ad90b
+md5: 3ffb447961508502fc81e063ca2071cb
 depends:
 - ncurses
 - libgcc >=14
 - ncurses >=6.6,<7.0a0
 license: BSD-2-Clause
 license_family: BSD
-size: 149007
-timestamp: 1786616643904
+size: 149680
+timestamp: 1791327362947
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libev-4.33-h80f16a2_3.conda
 sha256: 4475f79a020e9ff2a5a0308c48cb2970a25d55c3dd724a97ab28bfac3be6cd49
 md5: f679b30a53d410d0b5ae0cb8f5b7397e
@@ -349,25 +365,26 @@ license: MIT
 license_family: MIT
 size: 73118
 timestamp: 1786970733378
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpython-3.13.15-hc71fabe_103_cp313.conda
-build_number: 103
-sha256: e28273c2b900c86b63b07f8c3e17c16f2ebd276af66f9f235c2d0a175019f2f5
-md5: 5fc7f7a109f73cff181ab35949d94e30
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libpython-3.13.16-hc71fabe_101_cp313.conda
+build_number: 101
+sha256: e4d4201465c8ca783f0b6d8391ea40013b4c032976603245e0374a6483e0b9bf
+md5: e2597006486bb60c7e051a5c36bf6489
 depends:
 - libgcc >=15
 - libstdcxx >=15
 license: Python-2.0
-size: 8874379
-timestamp: 1788387711954
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.53.4-hd26f1b6_102.conda
-sha256: 08e6e0f7eae7174bf3e31009e4afebbbd227737248e3ef864b32c0d7698eba1c
-md5: 247ea3dd05990b9598af8accbf95c0ca
+size: 8873699
+timestamp: 1791334202339
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libsqlite-3.54.0-h399dd60_1.conda
+sha256: 8698cc6bcb3406d8bf06f674ce623ebb33a1f4c7a3adb56ced22efd34c96a928
+md5: 5c86b41aba07fab6aaeee5ac172bd30e
 depends:
+- icu >=78.3,<79.0a0
 - libgcc >=15
 - libzlib >=1.3.2,<2.0a0
 license: blessing
-size: 966570
-timestamp: 1791167229160
+size: 981485
+timestamp: 1791584316700
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libssh2-1.11.1-h7572e3e_1.conda
 sha256: f6fef76c1c8899d7976030871b8cd8016b0a306d2b8519834cd6491d6a42fb82
 md5: 833be3f226277d894df3c7a7131d9532
@@ -416,23 +433,23 @@ depends:
 license: X11 AND BSD-3-Clause
 size: 955422
 timestamp: 1786355019431
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.5.3-py313h6bbad23_0.conda
-sha256: efce638b7f5f06c9c9a0bc70e34a860768e2c34b6440268881fe0319c42703c2
-md5: ca453149f372afe9598b579b8b36f4d9
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.5.4-py313h6bbad23_0.conda
+sha256: 2fd147f26ef48e3a074291d9e8854011c3ec0eabfed135785348b3d68b73b44f
+md5: 6b60ac38b92a0991ffcd57254e3453d4
 depends:
 - python
 - libgcc >=15
 - libstdcxx >=15
-- liblapack >=3.9.0,<4.0a0
 - libblas >=3.9.0,<4.0a0
-- python_abi 3.13.* *_cp313
+- liblapack >=3.9.0,<4.0a0
 - libcblas >=3.9.0,<4.0a0
+- python_abi 3.13.* *_cp313
 constrains:
 - numpy-base <0a0
 license: BSD-3-Clause
 license_family: BSD
-size: 8072664
-timestamp: 1788731986173
+size: 8086200
+timestamp: 1791675322309
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/openssl-3.6.5-he6ad1d5_0.conda
 sha256: 238136f1df197ecd89bafd728a34d0642176f3170423d13d8276746d675a9485
 md5: 92aec5ec417d2ce9ae109e6c5ad377ff
@@ -493,31 +510,31 @@ license: MIT
 license_family: MIT
 size: 144124
 timestamp: 1772011987929
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.13.15-hd0fdf85_103_cp313.conda
-build_number: 103
-sha256: 26e18ba9ffeb63df902ef5bad7307835f3a729b9a490a38586f9adcbc3207c01
-md5: 9f7c225d204efc5be3b0a73e6b785cc4
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.13.16-hd0fdf85_101_cp313.conda
+build_number: 101
+sha256: b01f11d8816e9c5c0f35a191f56e38d0432d87a0dc1b99aa92dafd44f8670eab
+md5: 874041971606f2426a73eacdf76f0420
 depends:
 - bzip2 >=1.0.8,<2.0a0
 - ld_impl_linux-aarch64 >=2.36.1
-- libexpat >=2.8.1,<3.0a0
+- libexpat >=2.8.5,<3.0a0
 - libffi >=3.7.0,<3.8.0a0
 - libgcc >=15
 - liblzma >=5.8.3,<6.0a0
 - libmpdec >=4.0.0,<5.0a0
-- libpython 3.13.15 hc71fabe_103_cp313
+- libpython 3.13.16 hc71fabe_101_cp313
 - libsqlite >=3.53.4,<4.0a0
-- libuuid >=2.42.3,<3.0a0
+- libuuid >=2.42.4,<3.0a0
 - libzlib >=1.3.2,<2.0a0
 - ncurses >=6.6,<7.0a0
-- openssl >=3.5.8,<4.0a0
+- openssl >=3.5.9,<4.0a0
 - python_abi 3.13.* *_cp313
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
 license: Python-2.0
-size: 23454419
-timestamp: 1788387744112
+size: 23395059
+timestamp: 1791334237435
 python_site_packages_path: lib/python3.13/site-packages
 - conda: https://conda.anaconda.org/bioconda/linux-aarch64/python-edlib-1.3.9.post1-py313haca9121_3.conda
 sha256: 8a079243a5e21877e12bd2dbac3c53a7939fda49392c39de99dced4e70a1e1ee
diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml
index a7b52b1146b2..1cdd14f65b28 100644
--- a/modules/nf-core/sniffles/environment.yml
+++ b/modules/nf-core/sniffles/environment.yml
@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconda::htslib=1.24
   - bioconda::sniffles=2.8.1
diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf
index c3a76ad45f33..b10ee49ecb00 100644
--- a/modules/nf-core/sniffles/main.nf
+++ b/modules/nf-core/sniffles/main.nf
@@ -4,8 +4,8 @@ process SNIFFLES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6d/6de188cc5ba7548d54fc6d257336c8c6f57c9b403823b7ccc9978ca08d8d1945/data'
-:         'community.wave.seqera.io/library/sniffles:2.8.1--b8c26c44b42620c5' }"
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/21/211f5d256e62a50ad9c6806ce42da3dd11420f548a3307faa82068305cfcbfc2/data'
+:         'community.wave.seqera.io/library/htslib_sniffles:14a95caca8d8452b' }"
 
     input:
     tuple val(meta), path(input), path(index), path(genotype_vcf)
diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml
index f580a3528fcf..00bdb8bc287d 100644
--- a/modules/nf-core/sniffles/meta.yml
+++ b/modules/nf-core/sniffles/meta.yml
@@ -132,24 +132,24 @@ maintainers:
 containers:
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/sniffles:2.8.1--b8c26c44b42620c5
-      build_id: bd-b8c26c44b42620c5_1
-      scan_id: sc-be686545d29b5d3e_1
+      name: community.wave.seqera.io/library/htslib_sniffles:14a95caca8d8452b
+      build_id: bd-14a95caca8d8452b_1
+      scan_id: sc-edfb8dc7743dd1fc_1
     linux/arm64:
-      name: community.wave.seqera.io/library/sniffles:2.8.1--db3310e27781522c
-      build_id: bd-db3310e27781522c_1
-      scan_id: sc-47a2cf0d175ec349_1
+      name: community.wave.seqera.io/library/htslib_sniffles:0caddb2114424a6f
+      build_id: bd-0caddb2114424a6f_1
+      scan_id: sc-e40ae47ee821020d_1
   singularity:
-    linux/amd64:
-      name: oras://community.wave.seqera.io/library/sniffles:2.8.1--4efaba9191b482de
-      build_id: bd-4efaba9191b482de_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6d/6de188cc5ba7548d54fc6d257336c8c6f57c9b403823b7ccc9978ca08d8d1945/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/sniffles:2.8.1--d26f781cc4513316
-      build_id: bd-d26f781cc4513316_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/58fa6579cc0531a6a36d35c574ef3063c7afbd3f5549cc981a789c70175a7852/data
+      name: oras://community.wave.seqera.io/library/htslib_sniffles:d6622685f53e8d89
+      build_id: bd-d6622685f53e8d89_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0f/0fce44cce1f2abd393d39dfe4f80b15b780ade83f850a9739c73d3769dec0651/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/htslib_sniffles:576e74b26ca5211a
+      build_id: bd-576e74b26ca5211a_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/21/211f5d256e62a50ad9c6806ce42da3dd11420f548a3307faa82068305cfcbfc2/data
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-b8c26c44b42620c5_1.txt
+      lock_file: modules/nf-core/sniffles/.conda-lock/linux_amd64-bd-14a95caca8d8452b_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-db3310e27781522c_1.txt
+      lock_file: modules/nf-core/sniffles/.conda-lock/linux_arm64-bd-0caddb2114424a6f_1.txt

From 7cdcfb8495ba61195ab29979ca55a44349208062 Mon Sep 17 00:00:00 2001
From: Ksenia Lavrichenko <ksenia.lavrichenko@gmail.com>
Date: Tue, 13 Oct 2026 09:15:49 +0200
Subject: [PATCH 4/4] sniffles: decompress the genotype sites VCF with bgzip

---
 modules/nf-core/sniffles/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf
index b10ee49ecb00..672c3e4709fa 100644
--- a/modules/nf-core/sniffles/main.nf
+++ b/modules/nf-core/sniffles/main.nf
@@ -31,8 +31,8 @@ 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" : ''
+    // Sniffles reads the sites file as plain text, so a compressed one is decompressed first (fritzsedlazeck/Sniffles#613)
+    def decompress = genotype_vcf && genotype_vcf.name.endsWith('.gz') ? "bgzip -dc ${genotype_vcf} > ${prefix}.sites.vcf" : ''
     def genotype = genotype_vcf ? "--genotype-vcf ${genotype_vcf.name.endsWith('.gz') ? prefix + '.sites.vcf' : genotype_vcf}" : ''
 
     """