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39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
process IQTREE {
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tag "$alignment"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' :
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'quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0' }"
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input:
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path alignment
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val constant_sites
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output:
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path "*.treefile", 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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def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
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def memory = task.memory.toString().replaceAll(' ', '')
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"""
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iqtree \\
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$fconst_args \\
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$args \\
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-s $alignment \\
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-nt AUTO \\
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-ntmax $task.cpus \\
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-mem $memory \\
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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iqtree: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
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END_VERSIONS
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"""
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}
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