nf-core_modules/software/seacr/callpeak/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
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def VERSION = '1.3'
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process SEACR_CALLPEAK {
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), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::seacr=1.3=1 conda-forge::r-base=4.0.2=he766273_1 bioconda::bedtools=2.29.2=hc088bd4_0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
} else {
container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
}
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input:
tuple val(meta), path(bedgraph), path(ctrlbedgraph)
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output:
tuple val(meta), path("*.bed"), emit: bed
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
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SEACR_1.3.sh \\
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$bedgraph \\
$ctrlbedgraph \\
$options.args \\
$prefix
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echo $VERSION > ${software}.version.txt
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"""
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}