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77 lines
2.6 KiB
Text
77 lines
2.6 KiB
Text
process ENSEMBLVEP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' :
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'quay.io/biocontainers/ensembl-vep:106.1--pl5321h4a94de4_0' }"
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input:
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tuple val(meta), path(vcf)
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val genome
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val species
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val cache_version
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path cache
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path fasta
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path extra_files
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output:
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tuple val(meta), path("*.ann.vcf") , optional:true, emit: vcf
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tuple val(meta), path("*.ann.tab") , optional:true, emit: tab
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tuple val(meta), path("*.ann.json") , optional:true, emit: json
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tuple val(meta), path("*.ann.vcf.gz") , optional:true, emit: vcf_gz
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tuple val(meta), path("*.ann.tab.gz") , optional:true, emit: tab_gz
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tuple val(meta), path("*.ann.json.gz") , optional:true, emit: json_gz
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path "*.summary.html" , emit: report
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path "versions.yml" , emit: versions
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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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def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
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def compress_out = args.contains("--compress_output") ? '.gz' : ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
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def reference = fasta ? "--fasta $fasta" : ""
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"""
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vep \\
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-i $vcf \\
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-o ${prefix}.ann.${file_extension}${compress_out} \\
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$args \\
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$reference \\
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--assembly $genome \\
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--species $species \\
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--cache \\
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--cache_version $cache_version \\
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--dir_cache $dir_cache \\
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--fork $task.cpus \\
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--stats_file ${prefix}.summary.html \\
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.ann.vcf
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touch ${prefix}.ann.tab
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touch ${prefix}.ann.json
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touch ${prefix}.ann.vcf.gz
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touch ${prefix}.ann.tab.gz
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touch ${prefix}.ann.json.gz
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touch ${prefix}.summary.html
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
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END_VERSIONS
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"""
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}
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