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55 lines
2.4 KiB
Text
55 lines
2.4 KiB
Text
process SNIPPY_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2 ':
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'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }"
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input:
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tuple val(meta), path(reads)
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path reference
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output:
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tuple val(meta), path("${prefix}/${prefix}.tab") , emit: tab
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tuple val(meta), path("${prefix}/${prefix}.csv") , emit: csv
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tuple val(meta), path("${prefix}/${prefix}.html") , emit: html
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tuple val(meta), path("${prefix}/${prefix}.vcf") , emit: vcf
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tuple val(meta), path("${prefix}/${prefix}.bed") , emit: bed
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tuple val(meta), path("${prefix}/${prefix}.gff") , emit: gff
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tuple val(meta), path("${prefix}/${prefix}.bam") , emit: bam
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tuple val(meta), path("${prefix}/${prefix}.bam.bai") , emit: bai
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tuple val(meta), path("${prefix}/${prefix}.log") , emit: log
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tuple val(meta), path("${prefix}/${prefix}.aligned.fa") , emit: aligned_fa
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tuple val(meta), path("${prefix}/${prefix}.consensus.fa") , emit: consensus_fa
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tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa
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tuple val(meta), path("${prefix}/${prefix}.raw.vcf") , emit: raw_vcf
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tuple val(meta), path("${prefix}/${prefix}.filt.vcf") , emit: filt_vcf
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tuple val(meta), path("${prefix}/${prefix}.vcf.gz") , emit: vcf_gz
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tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi") , emit: vcf_csi
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tuple val(meta), path("${prefix}/${prefix}.txt") , emit: txt
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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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prefix = task.ext.prefix ?: "${meta.id}"
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def read_inputs = meta.single_end ? "--se ${reads[0]}" : "--R1 ${reads[0]} --R2 ${reads[1]}"
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"""
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snippy \\
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$args \\
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--cpus $task.cpus \\
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--outdir $prefix \\
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--reference $reference \\
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--prefix $prefix \\
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$read_inputs
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //')
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END_VERSIONS
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"""
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}
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