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39 lines
1 KiB
Text
39 lines
1 KiB
Text
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process KHMER_UNIQUEKMERS {
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tag "$fasta"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
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'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
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input:
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path fasta
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val kmer_size
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output:
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path "report.txt" , emit: report
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path "kmers.txt" , emit: kmers
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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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"""
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unique-kmers.py \\
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-k $kmer_size \\
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-R report.txt \\
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$args \\
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$fasta
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grep ^number report.txt | sed 's/^.*:.[[:blank:]]//g' > kmers.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
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END_VERSIONS
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"""
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}
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