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dysgu==1.6.4_version update (#5928)
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* all_files_update

* Update environment.yml

* update_meta.yml

* input==input_bam

* update_snapshot

* meta.yml,tags.yml update

* Update modules/nf-core/dysgu/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/dysgu/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/dysgu/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/dysgu/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* Update modules/nf-core/dysgu/meta.yml

Co-authored-by: Famke Bäuerle <[email protected]>

* update_author

---------

Co-authored-by: Famke Bäuerle <[email protected]>
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poddarharsh15 and famosab authored Jul 8, 2024
1 parent bf4f1b9 commit c274982
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7 changes: 7 additions & 0 deletions modules/nf-core/dysgu/environment.yml
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name: dysgu
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- dysgu
55 changes: 55 additions & 0 deletions modules/nf-core/dysgu/main.nf
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process DYSGU {
tag "$meta.id"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/dysgu:48830f55112c399e':
'community.wave.seqera.io/library/dysgu:faf71ac972284412' }"

input:
tuple val(meta), path(input), path(index)
tuple val(meta2), path(fasta), path(fai)

output:
tuple val(meta), path('*.vcf.gz') , emit: vcf
tuple val(meta), path('*.vcf.gz.tbi') , emit: tbi
path 'versions.yml' , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dysgu run \\
-p ${task.cpus} \\
-x \\
$fasta \\
. \\
$input \\
| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz
tabix ${args3} ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dysgu: \$(dysgu --version 2>&1)
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dysgu: \$(dysgu --version 2>&1)
END_VERSIONS
"""
}
68 changes: 68 additions & 0 deletions modules/nf-core/dysgu/meta.yml
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name: dysgu

description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
keywords:
- structural variants
- sv
- vcf
tools:
- dysgu:
description: Structural variant caller for mapped sequencing data
homepage: https://github.com/kcleal/dysgu
documentation: https://github.com/kcleal/dysgu/blob/master/README.rst
tool_dev_url: https://github.com/kcleal/dysgu
doi: "10.1093/nar/gkac039"
licence: ["GPL-3.0-or-later"]

input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1' ]`
- input:
type: file
description: Input BAM file
pattern: "*.bam"
- index:
type: file
description: BAM index file
pattern: "*.bai"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- meta2:
type: map
description: |
Groovy Map containing reference information
e.g. [ id:'genome' ]
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"

output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'sample1' ]
- vcf:
type: file
description: VCF file with identified structural variants
pattern: "*.{vcf.gz}"
- tbi:
type: file
description: The index of the BCF/VCF file
pattern: "*.{vcf.gz.tbi}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"

authors:
- "@famosab"
- "@poddarharsh15"
maintainers:
- "@poddarharsh15"
96 changes: 96 additions & 0 deletions modules/nf-core/dysgu/tests/main.nf.test
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nextflow_process {

name "Test Process DYSGU"
script "../main.nf"
process "DYSGU"
config "./nextflow.config"
tag "modules"
tag "modules_nfcore"
tag "dysgu"


test("human - bam") {

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

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() },
{ assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
)
}

}


test("human - cram") {

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

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() },
{ assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }
)
}

}


test("human - bam - stub") {

options "-stub"

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

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

}

}
75 changes: 75 additions & 0 deletions modules/nf-core/dysgu/tests/main.nf.test.snap
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{
"human - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
[
{
"id": "test"
},
"test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,cf1e0487502108690603dd16f034bf5e"
],
"tbi": [
[
{
"id": "test"
},
"test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,cf1e0487502108690603dd16f034bf5e"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T13:18:45.660262"
},
"human - bam": {
"content": [
[
"versions.yml:md5,cf1e0487502108690603dd16f034bf5e"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T13:19:56.62312"
},
"human - cram": {
"content": [
[
"versions.yml:md5,cf1e0487502108690603dd16f034bf5e"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T13:20:04.494134"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/dysgu/tests/nextflow.config
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process {
withName: DYSGU {
ext.args = '--exome '
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/dysgu/tests/tags.yml
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dysgu:
- "modules/nf-core/dysgu/**"

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