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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
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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conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' :
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'quay.io/biocontainers/graphmap:0.6.3--he513fc3_0' }"
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input:
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tuple val(meta), path(reads)
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path fasta
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path index
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output:
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tuple val(meta), path("*.sam"), emit: sam
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${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 ${prefix}.sam \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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