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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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name: dysgu | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
- defaults | ||
dependencies: | ||
- dysgu |
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process DYSGU { | ||
tag "$meta.id" | ||
label 'process_medium' | ||
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conda "${moduleDir}/environment.yml" | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'oras://community.wave.seqera.io/library/dysgu:48830f55112c399e': | ||
'community.wave.seqera.io/library/dysgu:faf71ac972284412' }" | ||
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input: | ||
tuple val(meta), path(input), path(index) | ||
tuple val(meta2), path(fasta), path(fai) | ||
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output: | ||
tuple val(meta), path('*.vcf.gz') , emit: vcf | ||
tuple val(meta), path('*.vcf.gz.tbi') , emit: tbi | ||
path 'versions.yml' , emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def args2 = task.ext.args2 ?: '' | ||
def args3 = task.ext.args3 ?: '' | ||
def prefix = task.ext.prefix ?: "${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 | ||
""" | ||
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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 | ||
""" | ||
} |
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name: dysgu | ||
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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"] | ||
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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}" | ||
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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" | ||
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authors: | ||
- "@famosab" | ||
- "@poddarharsh15" | ||
maintainers: | ||
- "@poddarharsh15" |
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nextflow_process { | ||
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name "Test Process DYSGU" | ||
script "../main.nf" | ||
process "DYSGU" | ||
config "./nextflow.config" | ||
tag "modules" | ||
tag "modules_nfcore" | ||
tag "dysgu" | ||
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test("human - bam") { | ||
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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) | ||
] | ||
""" | ||
} | ||
} | ||
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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") } | ||
) | ||
} | ||
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} | ||
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test("human - cram") { | ||
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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) | ||
] | ||
""" | ||
} | ||
} | ||
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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") } | ||
) | ||
} | ||
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} | ||
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test("human - bam - stub") { | ||
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options "-stub" | ||
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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) | ||
] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
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} |
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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" | ||
} | ||
} |
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process { | ||
withName: DYSGU { | ||
ext.args = '--exome ' | ||
} | ||
} |
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dysgu: | ||
- "modules/nf-core/dysgu/**" |