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1 process POLYPOLISH {
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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}${params.fs}polypolish${params.fs}0.5.0" : null)
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6 conda (params.enable_conda ? "bioconda::polypolish=0.5.0 conda-forge::libgcc-ng" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/polypolish:0.5.0--hdbdd923_4' :
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9 'quay.io/biocontainers/polypolish:0.5.0--hdbdd923_4' }"
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10
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11 input:
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12 tuple val(meta), path(genome), path(sam)
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13
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14 output:
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15 tuple val(meta), path("*.polished.fa"), emit: polished
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 """
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25
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26 polypolish \\
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27 $args \\
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28 $genome \\
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29 ${sam.join(' ')} > ${prefix}.polished.fa
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 polypolish: \$(echo \$(polypolish -V 2>&1) | sed 's/^Polypolish v//')
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34 END_VERSIONS
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35 """
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36 } |
