nf-core_modules/modules/atlas/pmd/main.nf

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process ATLAS_PMD {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
input:
tuple val(meta), path(bam), path(bai), path(pool_rg_txt)
path(fasta)
path(fai)
output:
tuple val(meta), path("*_PMD_input_Empiric.txt") , emit: empiric
tuple val(meta), path("*_PMD_input_Exponential.txt"), emit: exponential
tuple val(meta), path("*_PMD_Table_counts.txt") , emit: counts
tuple val(meta), path("*_PMD_Table.txt") , emit: table
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def pool_rg_txt = pool_rg_txt ? "poolReadGroups=${pool_rg_txt}" : ""
"""
atlas \\
$pool_rg_txt \\
task=PMD \\
bam=${bam} \\
fasta=${fasta} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')
END_VERSIONS
"""
}