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32 lines
850 B
Text
32 lines
850 B
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process GRAPHMAP2_INDEX {
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
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container "quay.io/biocontainers/graphmap:0.6.3--he513fc3_0"
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input:
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path(fasta)
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output:
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path("*.gmidx") ,emit: index
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path "*.version.txt" ,emit: version
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script:
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"""
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graphmap2 \\
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align \\
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-t $task.cpus \\
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-I \\
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-r $fasta
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echo \$(graphmap2 2>&1) > graphmap2.version.txt
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"""
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}
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