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sniffles: add forced calling (--genotype-vcf) #13111

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d0928c7
sniffles: add forced calling (--genotype-vcf) as an optional input
aksenia Oct 9, 2026
c0d4b44
sniffles: remove the Sniffles#615 note from the meta.yml description
aksenia Oct 9, 2026
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7 changes: 6 additions & 1 deletion modules/nf-core/sniffles/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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
Expand Down
8 changes: 7 additions & 1 deletion modules/nf-core/sniffles/meta.yml
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@@ -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.
keywords:
- sniffles
- structural-variant calling
Expand Down Expand Up @@ -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: |
Expand Down
132 changes: 124 additions & 8 deletions modules/nf-core/sniffles/tests/main.nf.test
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Expand Up @@ -8,6 +8,7 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "sniffles"
tag "gunzip"

test("homo_sapiens - [bam, bai], fasta, [], true, false") {

Expand All @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand Down Expand Up @@ -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' ],
Expand All @@ -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() }
)
}

}

}
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