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466ab67808
* Fix minimap2 index module * Fix minimap2 index tests * Fix graphmap2 index module * Fix graphmap2 module * Fix ECLint * Fix bedtools bamtobed module * Fix tests for bedtools bamtobed module * Add tag for graphmap2 align module * Fix EClint * Fix qcat module * Add md5sum for graphmap2/align module * Remove non-started test data file * Remove md5sum for graphmap2 align
46 lines
1.4 KiB
Text
46 lines
1.4 KiB
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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options = initOptions(params.options)
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process GRAPHMAP2_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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tag "$meta.id"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0"
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} else {
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container "quay.io/biocontainers/graphmap:0.6.3--he513fc3_0"
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}
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input:
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tuple val(meta), path(reads)
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path fasta
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path index
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output:
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tuple val(meta), path("*.sam"), emit: sam
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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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 $reads \\
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-o ${prefix}.sam \\
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$options.args
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echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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