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feat(sniffles): add optional regions input #13501

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4 changes: 3 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 @@ -11,7 +11,7 @@ process SNIFFLES {
: 'community.wave.seqera.io/library/htslib_sniffles:14a95caca8d8452b' }"

input:
tuple val(meta), path(input), path(index), path(genotype_vcf)
tuple val(meta), path(input), path(index), path(genotype_vcf), path(regions)
tuple val(meta2), path(fasta)
tuple val(meta3), path(tandem_file)
val(vcf_output)
Expand All @@ -32,6 +32,7 @@ process SNIFFLES {
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta}" : ""
def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : ''
def regions_bed = regions ? "--regions ${regions}" : ''
def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": ''
def snf = snf_output ? "--snf ${prefix}.snf": ''
// Sniffles reads the sites file as plain text, so a compressed one is decompressed first (fritzsedlazeck/Sniffles#613)
Expand All @@ -45,6 +46,7 @@ process SNIFFLES {
$reference \\
-t $task.cpus \\
$tandem_repeats \\
$regions_bed \\
$genotype \\
$vcf \\
$snf \\
Expand Down
6 changes: 6 additions & 0 deletions modules/nf-core/sniffles/meta.yml
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Expand Up @@ -36,6 +36,12 @@ input:
pattern: "*.{vcf,vcf.gz}"
ontologies:
- edam: http://edamontology.org/format_3016
- regions:
type: file
description: Optional BED file of regions to process. Sniffles only processes reads in these regions. Use an empty list (`[]`) to process all regions.
pattern: "*.bed"
ontologies:
- edam: http://edamontology.org/format_3003
- - meta2:
type: map
description: |
Expand Down
50 changes: 47 additions & 3 deletions modules/nf-core/sniffles/tests/main.nf.test
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Expand Up @@ -19,6 +19,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -55,6 +56,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -89,6 +91,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -126,6 +129,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -168,6 +172,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -201,6 +206,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -234,6 +240,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -267,6 +274,7 @@ nextflow_process {
[ 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),
[],
[]
]
input[1] = [
Expand Down Expand Up @@ -301,7 +309,8 @@ nextflow_process {
[ 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)
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] = [[], []]
Expand Down Expand Up @@ -347,7 +356,7 @@ nextflow_process {
[ 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 })
]).combine(GUNZIP.out.gunzip.map { _meta, vcf -> [vcf, []] })
input[1] = [[], []]
input[2] = [[], []]
input[3] = true
Expand Down Expand Up @@ -380,7 +389,8 @@ nextflow_process {
[ 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)
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] = [[], []]
Expand All @@ -399,4 +409,38 @@ nextflow_process {

}

test("homo_sapiens - nanopore [bam, bai, [], bed], [], [], true, false - regions") {

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(channel.of("chr2\t71600000\t71700000").collectFile(name: 'regions.bed', newLine: true))
input[1] = [[], []]
input[2] = [[], []]
input[3] = true
input[4] = false
"""
}
}

then {
def records = path(process.out.vcf.get(0).get(1)).linesGzip.findAll { line -> !line.startsWith("#") }
assertAll(
{ assert process.success },
{ assert records.every { line -> line.startsWith("chr2\t") } },
{ assert snapshot(
process.out.findAll { key, val -> key.startsWith("versions") },
file(process.out.tbi.get(0).get(1)).name,
records,
).match() }
)
}

}

}
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