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https://github.com/MillironX/nf-core_modules.git
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43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process SNAPALIGNER_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
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'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path("*.bam"), emit: bam
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tuple val(meta), path("*.bai"), optional: true, emit: bai
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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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def subcmd = meta.single_end ? "single" : "paired"
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"""
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INDEX=`dirname \$(find -L ./ -name "OverflowTable*")`
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[ -z "\$INDEX" ] && echo "Snap index files not found" 1>&2 && exit 1
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snap-aligner ${subcmd} \\
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\$INDEX \\
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${reads.join(" ")} \\
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-o ${prefix}.bam \\
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-t ${task.cpus} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
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END_VERSIONS
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"""
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}
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