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1 process MASH_SKETCH {
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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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
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9 'quay.io/biocontainers/mash:2.3--he348c14_1' }"
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10
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11 input:
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12 tuple val(meta), path(query)
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13
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14 output:
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15 tuple val(meta), path("*.msh") , emit: sketch
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16 tuple val(meta), path("*_mash_sketch.status"), emit: stats
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def queries = (query ? query.collect().join('\\n') : null)
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26 sleep(Math.round(params.genomes_chunk.toInteger()) as int * 100)
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27 """
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28 echo -e "$queries" > sketch_these.txt
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29
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30 mash \\
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31 sketch \\
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32 -p $task.cpus \\
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33 -o "msh.${task.index}.k${params.mashsketch_k}.${params.mashsketch_s}h.${prefix}" \\
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34 $args \\
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35 -l sketch_these.txt \\
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36 2> ${prefix}_${task.index}_mash_sketch.status
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37
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38 cat <<-END_VERSIONS > versions.yml
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39 "${task.process}":
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40 mash: \$( mash --version )
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41 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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42 END_VERSIONS
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43 """
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44 } |
