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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PANGOLIN {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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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=3.1.11' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1'
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} else {
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container 'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1'
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}
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path('*.csv'), emit: report
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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pangolin \\
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$fasta\\
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--outfile ${prefix}.pangolin.csv \\
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--threads $task.cpus \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(pangolin --version | sed "s/pangolin //g")
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END_VERSIONS
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"""
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}
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