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41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process KHMER_NORMALIZEBYMEDIAN {
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tag "${name}"
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label 'process_long'
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conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null)
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container "${ 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 pe_reads
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path se_reads
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val name
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output:
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path "${name}.fastq.gz", emit: reads
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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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pe_args = pe_reads ? "--paired" : ""
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se_args = se_reads ? "--unpaired-reads ${se_reads}" : ""
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files = pe_reads ? pe_reads : se_reads
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"""
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normalize-by-median.py \\
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-M ${task.memory.toGiga()}e9 \\
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--gzip $args \\
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-o ${name}.fastq.gz \\
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$pe_args \\
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$se_args \\
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$files
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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khmer: \$( normalize-by-median.py --version 2>&1 | grep ^khmer | sed 's/^khmer //' )
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END_VERSIONS
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"""
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}
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