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kkonganti@105
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1 process SPADES_ASSEMBLE {
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kkonganti@105
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2 tag "$meta.id"
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kkonganti@105
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3 label 'process_higher'
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kkonganti@105
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4
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kkonganti@105
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null)
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kkonganti@105
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6 conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
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kkonganti@105
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@105
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8 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
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kkonganti@105
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9 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
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kkonganti@105
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10
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kkonganti@105
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11 input:
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kkonganti@105
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12 tuple val(meta), path(illumina), path(pacbio), path(nanopore)
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kkonganti@105
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13
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kkonganti@105
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14 output:
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kkonganti@105
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15 path "${meta.id}${params.fs}*"
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kkonganti@105
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16 tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true
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kkonganti@105
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17 tuple val(meta), path("${meta.id}${params.fs}spades.log") , emit: log
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kkonganti@105
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18 path "versions.yml" , emit: versions
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kkonganti@105
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19
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kkonganti@105
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20 when:
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kkonganti@105
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21 task.ext.when == null || task.ext.when
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kkonganti@105
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22
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kkonganti@105
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23 script:
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kkonganti@105
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24 def args = task.ext.args ?: ''
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kkonganti@105
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@105
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26 def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : ""
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kkonganti@105
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27 def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
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kkonganti@105
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28 def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
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kkonganti@105
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29 def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
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kkonganti@105
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30 def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : ""
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kkonganti@105
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31 """
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kkonganti@105
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32 spades.py \\
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kkonganti@105
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33 $args \\
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kkonganti@105
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34 --threads $task.cpus \\
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kkonganti@105
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35 $maxmem \\
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kkonganti@105
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36 $custom_hmms \\
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kkonganti@105
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37 $illumina_reads \\
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kkonganti@105
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38 $pacbio_reads \\
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kkonganti@105
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39 $nanopore_reads \\
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kkonganti@105
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40 -o ${prefix}
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kkonganti@105
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41
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kkonganti@105
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42 cat <<-END_VERSIONS > versions.yml
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kkonganti@105
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43 "${task.process}":
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kkonganti@105
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44 spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
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kkonganti@105
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45 END_VERSIONS
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kkonganti@105
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46 """
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kkonganti@105
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47 } |
