/
main.nf
42 lines (36 loc) · 1.32 KB
/
main.nf
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process HOMER_ANNOTATEPEAKS {
tag "$meta.id"
label 'process_medium'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
'biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(peak)
path fasta
path gtf
output:
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
tuple val(meta), path("*annStats.txt"), emit: stats, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
annotatePeaks.pl \\
$peak \\
$fasta \\
$args \\
-gtf $gtf \\
-cpu $task.cpus \\
> ${prefix}.annotatePeaks.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
homer: $VERSION
END_VERSIONS
"""
}