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35 lines
873 B
Plaintext
35 lines
873 B
Plaintext
process BBMAP_INDEX {
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tag "$fasta"
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label 'process_long'
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conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0' :
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'quay.io/biocontainers/bbmap:38.92--he522d1c_0' }"
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input:
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path fasta
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output:
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path 'ref' , 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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bbmap.sh \\
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ref=${fasta} \\
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$args \\
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threads=$task.cpus \\
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-Xmx${task.memory.toGiga()}g
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bbmap: \$(bbversion.sh)
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END_VERSIONS
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"""
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}
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