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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process PORECHOP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
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'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: reads
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tuple val(meta), path("*.log") , emit: log
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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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porechop \\
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-i $reads \\
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-t $task.cpus \\
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$args \\
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-o ${prefix}.fastq.gz \\
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> ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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porechop: \$( porechop --version )
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END_VERSIONS
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"""
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}
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