nf-core_modules/modules/methyldackel/extract/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process METHYLDACKEL_EXTRACT {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
} else {
container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.bedGraph"), emit: bedgraph
path "versions.yml" , emit: versions
script:
"""
MethylDackel extract \\
$options.args \\
$fasta \\
$bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
END_VERSIONS
"""
}