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53 lines
1.5 KiB
Text
53 lines
1.5 KiB
Text
process ULTRA_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4 bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0':
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'quay.io/biocontainers/mulled-v2-4b749ef583d6de806ddbf51c2d235ac8c14763c6:f63170074b42f54276c1f9b334e732a0f3bf28bd-0' }"
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input:
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tuple val(meta), path(reads)
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path genome
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tuple path(pickle), path(db)
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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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"""
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uLTRA \\
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align \\
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--t $task.cpus \\
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--prefix $prefix \\
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--index ./ \\
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$args \\
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$genome \\
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$reads \\
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./
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samtools \\
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sort \\
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--threads $task.cpus \\
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-o ${prefix}.bam \\
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-O BAM \\
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$args2 \\
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${prefix}.sam
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rm ${prefix}.sam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ultra: \$( uLTRA --version|sed 's/uLTRA //g' )
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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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