nf-core_modules/modules/hmmcopy/readcounter/main.nf
Simon Pearce 374d81e0b3
readcounter module for hmmcopy (#1001)
* readcounter module for hmmcopy

* Changed version number

* Fix indentation

* Update main.nf

* Update modules/hmmcopy/readcounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 11:01:13 +00:00

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1.3 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '0.1.1'
process HMMCOPY_READCOUNTER {
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::hmmcopy=0.1.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
} else {
container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
}
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.wig"), emit: wig
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
readCounter \\
$options.args \\
${bam} > ${prefix}.wig
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo $VERSION)
END_VERSIONS
"""
}