nf-core_modules/modules/fasttree/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FASTTREE {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4"
} else {
container "quay.io/biocontainers/fasttree:2.1.10--h516909a_4"
}
input:
path alignment
output:
path "*.tre", emit: phylogeny
path "versions.yml" , emit: versions
script:
"""
fasttree \\
$options.args \\
-log fasttree_phylogeny.tre.log \\
-nt $alignment \\
> fasttree_phylogeny.tre
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/')
END_VERSIONS
"""
}