mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
37 lines
1 KiB
Text
37 lines
1 KiB
Text
process SVDB_QUERY {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
|
|
'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf)
|
|
path (vcf_db)
|
|
|
|
output:
|
|
tuple val(meta), path("*_ann_svdbq.vcf"), emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
svdb \\
|
|
--query \\
|
|
$args \\
|
|
--db $vcf_db \\
|
|
--query_vcf $vcf \\
|
|
>${prefix}_ann_svdbq.vcf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|