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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
process ULTRA_PIPELINE {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' :
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'quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_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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path gtf
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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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uLTRA \\
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pipeline \\
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--t $task.cpus \\
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--prefix $prefix \\
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$args \\
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$genome \\
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$gtf \\
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$reads \\
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./
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ultra: \$( uLTRA --version|sed 's/uLTRA //g' )
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END_VERSIONS
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"""
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}
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