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45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
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process BISCUIT_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
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'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
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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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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 args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
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def samtools_cpus = task.cpus-biscuit_cpus
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"""
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INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
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biscuit align \\
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$args \\
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-@ $biscuit_cpus \\
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\$INDEX \\
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$reads \\
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| samtools sort $args2 --threads $samtools_cpus -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
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samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
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END_VERSIONS
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"""
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}
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