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1 process ABRICATE_RUN {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
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6 conda (params.enable_conda ? "conda-forge::perl bioconda::abricate=1.0.1" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/abricate:1.0.1--ha8f3691_1':
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9 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
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10
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11 input:
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12 tuple val(meta), path(assembly)
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13 val abdbs
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14
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15 output:
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16 path "${meta.id}${params.fs}*"
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17 tuple val(meta), path("${meta.id}${params.fs}*.ab.txt"), emit: abricated
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18 path "versions.yml" , emit: versions
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19
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20 when:
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21 (task.ext.when == null || task.ext.when) && assembly.size() > 0
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 def dbs = abdbs.collect().join('\\n')
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27 """
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28 newprefix="${prefix}${params.fs}${prefix}"
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29
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30 if [ ! -d "$prefix" ]; then
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31 mkdir "$prefix" || exit 1
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32 fi
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33
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34 echo -e "$dbs" | while read -r db; do
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35 abricate \\
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36 $assembly \\
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37 $args \\
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38 --db \$db \\
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39 --threads $task.cpus 1> "\${newprefix}.\${db}.ab.txt"
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40 done
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41
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42 cat <<-END_VERSIONS > versions.yml
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43 "${task.process}":
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44 abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
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45 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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46 END_VERSIONS
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47 """
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48 } |
