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1 process MASURCA_POLISH {
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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}${params.fs}masurca${params.fs}4.1.0" : null)
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6 conda (params.enable_conda ? "bioconda::masurca=4.1.0 conda-forge::libgcc-ng" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/masurca:4.1.0--pl5321hb5bd705_1' :
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9 'quay.io/biocontainers/masurca:4.1.0--pl5321hb5bd705_1' }"
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10
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11 input:
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12 tuple val(meta), path(contigs), path(reads)
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13
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14 output:
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15 tuple val(meta), path("${prefix}_contigs.fa"), emit: polished
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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 memory = (task.memory ? task.memory.toGiga() : 16)
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24 def mem_per_thread = memory.toGiga().toInteger().div(task.cpus.toInteger()).round(0)
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25 def all_reads = "${reads.join(' ')}"
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26 prefix = (task.ext.prefix ?: meta.id)
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27 """
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28 polca.sh \\
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29 -a $contigs \\
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30 -r '${all_reads}' \\
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31 -t $task.cpus \\
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32 -m $mem_per_thread \\
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33 $args \\
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34
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35 mv 'contigs.fa' "${prefix}.contigs.fa"
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36
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37 cat <<-END_VERSIONS > versions.yml
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38 "${task.process}":
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39 masurca: \$(echo \$(masurca --version 2>&1) | sed 's/^.*version //')
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40 END_VERSIONS
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41 """
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42 } |
