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33 lines
933 B
Text
33 lines
933 B
Text
process FASTTREE {
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' :
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'quay.io/biocontainers/fasttree:2.1.10--h516909a_4' }"
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input:
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path alignment
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output:
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path "*.tre", emit: phylogeny
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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fasttree \\
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$args \\
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-log fasttree_phylogeny.tre.log \\
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-nt $alignment \\
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> fasttree_phylogeny.tre
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fasttree: \$(fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/')
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END_VERSIONS
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"""
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}
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