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39 lines
1.1 KiB
Plaintext
39 lines
1.1 KiB
Plaintext
process MEGAN_RMA2INFO {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::megan=6.21.7"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
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'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
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input:
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tuple val(meta), path(rma6)
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val(megan_summary)
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output:
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tuple val(meta), path("*.txt.gz") , emit: txt
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tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
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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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def summary = megan_summary ? "-es ${prefix}.megan" : ""
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"""
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rma2info \\
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-i ${rma6} \\
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-o ${prefix}.txt.gz \\
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${summary} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
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END_VERSIONS
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"""
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}
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