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1 process MEGAHIT_ASSEMBLE {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
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6 conda (params.enable_conda ? "bioconda::megahit=1.2.9" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
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9 'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, optional: true
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 def maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : ""
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25 if (meta.single_end) {
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26 """
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27 megahit \\
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28 -r ${reads} \\
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29 -t $task.cpus \\
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30 $maxmem \\
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31 $args \\
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32 --out-dir $prefix \\
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33 --out-prefix $prefix
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34
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35 cat <<-END_VERSIONS > versions.yml
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36 "${task.process}":
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37 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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38 END_VERSIONS
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39 """
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40 } else {
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41 """
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42 megahit \\
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43 -1 ${reads[0]} \\
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44 -2 ${reads[1]} \\
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45 -t $task.cpus \\
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46 $maxmem \\
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47 $args \\
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48 --out-dir $prefix \\
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49 --out-prefix $prefix
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50
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51 cat <<-END_VERSIONS > versions.yml
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52 "${task.process}":
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53 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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54 END_VERSIONS
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55 """
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56 }
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57 }
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