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212177d479
* output constant sites as a val as well as a file so it can be passed into iqtree * Using an env variable because that's far safer! * Update software/snpsites/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } 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 "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0"
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} else {
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container "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
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}
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input:
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path alignment
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output:
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path "*.fas" , emit: fasta
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path "*.sites.txt" , emit: constant_sites
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path "*.version.txt", emit: version
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env CONSTANT_SITES, emit: constant_sites_string
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script:
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def software = getSoftwareName(task.process)
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"""
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snp-sites -c \\
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$alignment \\
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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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echo \$(snp-sites -V 2>&1) | sed 's/snp-sites //' > ${software}.version.txt
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"""
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}
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