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37 lines
1.4 KiB
Text
37 lines
1.4 KiB
Text
process SAMBLASTER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' :
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'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }"
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input:
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tuple val(meta), path(bam)
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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 args3 = task.ext.args3 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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"""
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samtools view -h $args2 $bam | \\
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samblaster $args | \\
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samtools view $args3 -Sb - >${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samblaster: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' )
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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