mirror of
https://github.com/MillironX/taxprofiler.git
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41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
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process KRONA_CLEANUP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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'biocontainers/biocontainers:v1.2.0_cv1' }"
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input:
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tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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# Copy the file to a new name
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cp ${krona} ${prefix}.txt
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# Remove ugly 'x__' prefixes for each of the taxonomic levels
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LEVELS=(d k p c o f g s)
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for L in "\${LEVELS[@]}"; do
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sed -i "s/\${L}__//g" ${prefix}.txt
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done
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# Remove underscores that are standing in place of spaces
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sed -i "s/_/ /g" ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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