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a8720463ac
* add graphmap index module * add graphmap2/index * add graohmap2 align module * remove graphmap2 align md5sum
35 lines
937 B
Text
35 lines
937 B
Text
// 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_ALIGN {
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tag "$meta.id"
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publishDir "${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), meta:meta, publish_by_meta:['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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tuple val(meta), path(fastq)
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path(fasta)
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path(index)
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output:
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tuple val(meta), path("*.sam"), emit: align_sam
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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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-r $fasta \\
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-i $index \\
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-d $fastq \\
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-o ${meta.id}.sam \\
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--extcigar
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"""
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}
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