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35 lines
962 B
Plaintext
35 lines
962 B
Plaintext
process KRONA_KTIMPORTTEXT {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::krona=2.8.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
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'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
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input:
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tuple val(meta), path(report)
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output:
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tuple val(meta), path ('*.html'), emit: html
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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 args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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ktImportText \\
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$args \\
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-o ${prefix}.html \\
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$report
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
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END_VERSIONS
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"""
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}
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