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

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process BEDTOOLS_GENOMECOV {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
input:
tuple val(meta), path(intervals), val(scale)
path sizes
val extension
output:
tuple val(meta), path("*.${extension}"), emit: genomecov
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args_list = args.tokenize()
args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
args += " -bg"
}
def prefix = task.ext.prefix ?: "${meta.id}"
if (intervals.name =~ /\.bam/) {
"""
bedtools \\
genomecov \\
-ibam $intervals \\
$args \\
> ${prefix}.${extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
} else {
"""
bedtools \\
genomecov \\
-i $intervals \\
-g $sizes \\
$args \\
> ${prefix}.${extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
}
}