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31 lines
912 B
Text
31 lines
912 B
Text
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process BOWTIE2_BUILD {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
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'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
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input:
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path fasta
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output:
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path 'bowtie2' , emit: index
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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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"""
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mkdir bowtie2
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bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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