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https://github.com/MillironX/nf-core_modules.git
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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
46 lines
1.5 KiB
Text
46 lines
1.5 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 SNPSITES {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0"
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} else {
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container "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
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}
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input:
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path alignment
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output:
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path "*.fas" , emit: fasta
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path "*.sites.txt" , emit: constant_sites
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path "versions.yml" , emit: version
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env CONSTANT_SITES, emit: constant_sites_string
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script:
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def software = getSoftwareName(task.process)
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"""
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snp-sites \\
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$alignment \\
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$options.args \\
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> filtered_alignment.fas
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echo \$(snp-sites -C $alignment) > constant.sites.txt
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CONSTANT_SITES=\$(cat constant.sites.txt)
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
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END_VERSIONS
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"""
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}
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