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Merged
bagnacan merged 8 commits into from
Apr 1, 2026
Merged

Bump delly call #11080

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d30f78f
Bump delly version
bagnacan Mar 27, 2026
92a5a79
Make use of threads
bagnacan Mar 27, 2026
86979c9
Replace unallowed key
bagnacan Mar 30, 2026
a356134
Create dedicated vcf/bcf channel
bagnacan Mar 31, 2026
50795d2
Adapt tests to new vcf/bcf channel
bagnacan Mar 31, 2026
a925623
Merge branch 'master' into bump-delly-call
bagnacan Apr 1, 2026
0627d31
Update test snapshot
bagnacan Apr 1, 2026
5a1cb19
Merge branch 'master' into bump-delly-call
bagnacan Apr 1, 2026
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2 changes: 1 addition & 1 deletion modules/nf-core/delly/call/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::delly=1.3.3
- bioconda::delly=1.7.3
8 changes: 4 additions & 4 deletions modules/nf-core/delly/call/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,14 @@ process DELLY_CALL {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/delly:1.3.3--h4d20210_0' :
'biocontainers/delly:1.3.3--h4d20210_0' }"
'https://depot.galaxyproject.org/singularity/delly:1.7.3--hd6466ae_0' :
'biocontainers/delly:1.7.3--hd6466ae_0' }"

input:
tuple val(meta), path(input), path(input_index), path(vcf), path(vcf_index), path(exclude_bed)
tuple val(meta2), path(fasta)
tuple val(meta3), path(fai)
val(suffix)

output:
tuple val(meta), path("*.{bcf,vcf.gz}") , emit: bcf
Expand All @@ -24,7 +25,6 @@ process DELLY_CALL {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "bcf"

def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""

Expand All @@ -37,6 +37,7 @@ process DELLY_CALL {
delly \\
call \\
${args} \\
--threads ${task.cpus} \\
${bcf_output} \\
--genome ${fasta} \\
${genotype} \\
Expand All @@ -47,7 +48,6 @@ process DELLY_CALL {

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "bcf"

def bcf_output = suffix == "bcf" ? "touch ${prefix}.bcf && touch ${prefix}.bcf.csi" : ""
def vcf_output = suffix == "vcf" ? "echo '' | gzip > ${prefix}.vcf.gz && touch ${prefix}.vcf.gz.tbi" : ""
Expand Down
11 changes: 9 additions & 2 deletions modules/nf-core/delly/call/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,13 @@ input:
description: Index of reference fasta file to identify split-reads
pattern: "*.fai"
ontologies: []
- suffix:
type: string
description: A flag to specify whether the output should be in BCF or VCF
format
enum:
- "bcf"
- "vcf"
output:
bcf:
- - meta:
Expand All @@ -78,8 +85,8 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.{bcf,vcf.gz}":
type: file
description: Called variants in BCF/VCF format. Specify either "bcf" or
"vcf" in ext.suffix to define the output type
description: Called variants in BCF/VCF format. Set suffix to either
"bcf" or "vcf" to define the output type
pattern: "*.{bcf,vcf.gz}"
ontologies: []
csi:
Expand Down
119 changes: 112 additions & 7 deletions modules/nf-core/delly/call/tests/main.nf.test
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Expand Up @@ -9,9 +9,42 @@ nextflow_process {
tag "delly"
tag "delly/call"

test("homo_sapiens - bam, bai, [], [], [], fasta, fai") {
test("homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf") {

config "./vcf.config"
when {
process {
"""
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
[],
[],
[]
]
input[1] = [
[ id:'fasta' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
]
input[2] = [
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'vcf'
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

test("homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf") {

when {
process {
Expand All @@ -32,6 +65,7 @@ nextflow_process {
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'bcf'
"""
}
}
Expand All @@ -42,10 +76,78 @@ nextflow_process {
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}

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

when {
process {
"""
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
[],
[],
[]
]
input[1] = [
[ id:'fasta' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
]
input[2] = [
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = ''
"""
}
}

then {
assertAll(
{ assert !process.success },
)
}
}

test("homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf - config") {

config "./nextflow.config"

when {
process {
"""
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
[],
[],
[]
]
input[1] = [
[ id:'fasta' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
]
input[2] = [
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'bcf'
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}

test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
test("homo_sapiens - cram, crai, [], [], [], fasta, fai, bcf") {

when {
process {
Expand All @@ -66,6 +168,7 @@ nextflow_process {
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'bcf'
"""
}
}
Expand All @@ -79,7 +182,7 @@ nextflow_process {

}

test("homo_sapiens - cram, crai, [], [], bed, fasta, fai") {
test("homo_sapiens - cram, crai, [], [], bed, fasta, fai, bcf") {

when {
process {
Expand All @@ -100,6 +203,7 @@ nextflow_process {
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'bcf'
"""
}
}
Expand All @@ -113,7 +217,7 @@ nextflow_process {

}

test("homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai") {
test("homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai, bcf") {

when {
process {
Expand All @@ -134,6 +238,7 @@ nextflow_process {
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'bcf'
"""
}
}
Expand All @@ -147,9 +252,8 @@ nextflow_process {

}

test("homo_sapiens - bam, bai, [], [], [], fasta, fai - stub") {
test("homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf - stub") {

config "./vcf.config"
options "-stub"

when {
Expand All @@ -171,6 +275,7 @@ nextflow_process {
[ id:'fai' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
]
input[3] = 'vcf'
"""
}
}
Expand Down
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