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32 lines
995 B
Text
32 lines
995 B
Text
process KRAKEN2_STANDARD_REPORT {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? 'conda-forge::sed=4.8' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
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'biocontainers/biocontainers:v1.2.0_cv2' }"
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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(result), emit: report
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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 ?: "${meta.id}"
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result = "${prefix}_standardized.kraken2.report.txt"
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"""
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cut -f1-3,6-8 '${report}' > '${result}'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cut: \$(echo \$(cut --version 2>&1) | sed 's/^.*(GNU coreutils) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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