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45 lines
1.2 KiB
Text
45 lines
1.2 KiB
Text
process QUAST {
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' :
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'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
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input:
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path consensus
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path fasta
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path gff
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val use_fasta
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val use_gff
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output:
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path "${prefix}" , emit: results
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path '*.tsv' , emit: tsv
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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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prefix = task.ext.prefix ?: 'quast'
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def features = use_gff ? "--features $gff" : ''
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def reference = use_fasta ? "-r $fasta" : ''
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"""
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quast.py \\
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--output-dir $prefix \\
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$reference \\
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$features \\
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--threads $task.cpus \\
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$args \\
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${consensus.join(' ')}
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ln -s ${prefix}/report.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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