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1 process MEDAKA_CONSENSUS {
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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}${params.fs}medaka${params.fs}1.11.2" : null)
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6 conda (params.enable_conda ? "bioconda::medaka=1.11.2 conda-forge::python" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/medaka:1.11.2--py310h87e71ce_0' :
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9 'quay.io/biocontainers/medaka:1.11.2--py310h87e71ce_0' }"
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10
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11 input:
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12 tuple val(meta), path(bam), path(bai)
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13
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14 output:
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15 tuple val(meta), path("*.hdr"), emit: hdr
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 """
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25 medaka consensus \\
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26 --threads $task.cpus \\
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27 $args \\
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28 $bam \\
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29 ${prefix}.medaka.hdr
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 medaka: \$( medaka --version 2> /dev/null | sed 's/medaka //g' )
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34 END_VERSIONS
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35 """
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36 } |
