nf-core_modules/software/pangolin/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process PANGOLIN {
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']) }
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conda (params.enable_conda ? 'bioconda::pangolin=2.4.2' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/pangolin:2.4.2--pyhdfd78af_0'
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} else {
container 'quay.io/biocontainers/pangolin:2.4.2--pyhdfd78af_0'
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}
input:
tuple val(meta), path(fasta)
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output:
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tuple val(meta), path('*.csv'), emit: report
path '*.version.txt' , emit: version
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script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
"""
pangolin \\
$fasta\\
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--outfile ${prefix}.pangolin.csv \\
--threads $task.cpus \\
$options.args
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pangolin --version | sed "s/pangolin //g" > ${software}.version.txt
"""
}