nf-core_modules/software/methyldackel/mbias/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

44 lines
1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process METHYLDACKEL_MBIAS {
tag "$meta.id"
label 'process_low'
publishDir "${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=0.5.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.2--h7435645_0"
} else {
container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.mbias.txt"), emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
MethylDackel mbias \\
$options.args \\
$fasta \\
$bam \\
$prefix \\
--txt \\
> ${prefix}.mbias.txt
echo \$(MethylDackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
"""
}