nf-core_modules/modules/pydamage/analyze/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PYDAMAGE_ANALYZE {
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::pydamage=0.62" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0"
}
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
pydamage \\
analyze \\
$options.args \\
-p $task.cpus \\
$bam
echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g' > ${software}.version.txt
"""
}