nf-core_modules/modules/variantbam/main.nf
2022-02-04 09:53:32 +01:00

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Text

def VERSION = '1.4.4a' // Version information not provided by tool on CLI
process VARIANTBAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' :
'quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bam"), emit: bam
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}"
"""
variant \\
$bam \\
-o ${prefix}.bam \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
variantbam: $VERSION
END_VERSIONS
"""
}