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38 lines
1 KiB
Text
38 lines
1 KiB
Text
process SNPSITES {
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' :
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'quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0' }"
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input:
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path alignment
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output:
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path "*.fas" , emit: fasta
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path "*.sites.txt" , emit: constant_sites
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path "versions.yml" , emit: versions
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env CONSTANT_SITES, emit: constant_sites_string
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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snp-sites \\
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$alignment \\
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$args \\
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> filtered_alignment.fas
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echo \$(snp-sites -C $alignment) > constant.sites.txt
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CONSTANT_SITES=\$(cat constant.sites.txt)
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snpsites: \$(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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