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1 process SEQTK_SEQ {
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2 tag "$meta.id"
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3 label 'process_mem_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqtk${params.fs}1.3-r106" : null)
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6 conda (params.enable_conda ? "bioconda::seqtk=1.3 conda-forge::gzip" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
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9 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
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10
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11 input:
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12 tuple val(meta), path(fastx)
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13
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14 output:
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15 tuple val(meta), path("*.gz"), emit: fastx
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24
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25 def extension = "fastq"
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26 if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) {
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27 extension = "fasta"
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28 }
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29 """
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30 seqtk \\
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31 seq \\
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32 $args \\
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33 $fastx | \\
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34 gzip -c > ${prefix}.seqtk-seq.${task.index}.${extension}.gz
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35
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36 cat <<-END_VERSIONS > versions.yml
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37 "${task.process}":
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38 seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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39 gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' )
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40 END_VERSIONS
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41 """
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42 } |
