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1 process BBTOOLS_BBMERGE {
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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}${params.fs}bbtools${params.fs}38.94" : null)
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6 conda (params.enable_conda ? "conda-forge::pbzip2 bioconda::bbmap=38.95" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/bbmap:38.95--he522d1c_0' :
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9 'quay.io/biocontainers/bbmap:38.95--he522d1c_0' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path("*.fastq.gz"), emit: fastq
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16 tuple val(meta), path("*.log") , emit: log
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 !meta.single_end
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def in_files = "in1=${reads[0]} in2=${reads[1]}"
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26 def out_file = "out=${prefix}.bbmerge.fastq.gz"
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27 def adapters_file = file (meta.adapters)
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28 def adapters = !("${adapters_file.simpleName}" ==~ 'dummy_file.*') && adapters_file.exits() ? "adapters=${meta.adapters}" : ''
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29 def args_formatted = args.replaceAll('=\s+', '=')
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30 """
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31 bbmerge.sh \\
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32 -Xmx${task.memory.toGiga()}G \\
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33 threads=$task.cpus \\
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34 $args_formatted \\
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35 $adapters \\
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36 $in_files \\
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37 $out_file &> ${prefix}.bbmerge.log
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38
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39 cat <<-END_VERSIONS > versions.yml
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40 "${task.process}":
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41 bbmerge: \$( bbversion.sh )
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42 END_VERSIONS
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43 """
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44 }
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