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1 process FILTLONG {
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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}${params.fs}filtlong${params.fs}0.2.1" : null)
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6 conda (params.enable_conda ? "conda-forge::gcc bioconda::filtlong=0.2.1" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
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9 'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
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10
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11 input:
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12 tuple val(meta), path(shortreads), path(longreads)
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13
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14 output:
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15 tuple val(meta), path("*.filtlong.fastq.gz"), emit: filtered_reads
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16 tuple val(meta), path("*.filtlong.log") , emit: log
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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26 if ("$longreads" == "${prefix}.filtlong.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
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27 """
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28 filtlong \\
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29 $short_reads \\
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30 $args \\
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31 $longreads \\
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32 2> >(tee ${prefix}.filtlong.log >&2) \\
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33 | gzip -n > ${prefix}.filtlong.fastq.gz
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34
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35 cat <<-END_VERSIONS > versions.yml
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36 "${task.process}":
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37 filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
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38 END_VERSIONS
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39 """
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40 } |
