nf-core_modules/modules/snpsift/split/main.nf

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process SNPSIFT_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' :
'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }"
input:
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.vcf"), emit: out_vcfs
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.split) {
"""
SnpSift \\
split \\
$args \\
$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
END_VERSIONS
"""
} else {
"""
SnpSift \\
split \\
-j \\
$args \\
$vcf \\
> ${prefix}.joined.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
END_VERSIONS
"""
}
}