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0
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1 process MASH_SCREEN {
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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}${params.fs}mash${params.fs}2.3" : null)
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6 conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
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9 'quay.io/biocontainers/mash:2.3--he348c14_1' }"
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10
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11 input:
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12 tuple val(meta), path(query)
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13
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14 output:
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15 tuple val(meta), path("*.screened"), emit: screened
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 def sequence_sketch = (meta.sequence_sketch ?: '')
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25 """
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26 mash \\
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27 screen \\
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28 $args \\
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29 -p $task.cpus \\
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30 $sequence_sketch \\
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31 $query \\
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32 > ${prefix}.screened
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33
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34 cat <<-END_VERSIONS > versions.yml
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35 "${task.process}":
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36 mash: \$( mash --version )
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37 END_VERSIONS
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38 """
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39 } |
