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34 lines
989 B
Text
34 lines
989 B
Text
process RAXMLNG {
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' :
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'quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0' }"
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input:
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path alignment
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output:
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path "*.raxml.bestTree", emit: phylogeny
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path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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raxml-ng \\
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$args \\
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--msa $alignment \\
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--threads $task.cpus \\
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--prefix output
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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raxmlng: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
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END_VERSIONS
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"""
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}
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