nf-core_modules/software/rapidnj/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process RAPIDNJ {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
} else {
container "quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
}
input:
path alignment
output:
path "*.sth" , emit: stockholm_alignment
path "*.tre" , emit: phylogeny
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
python \\
-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
rapidnj \\
alignment.sth \\
$options.args \\
-i sth \\
-c $task.cpus \\
-x rapidnj_phylogeny.tre
# Doesn't appear to be a way of getting the version number
echo 2.3.2 > ${software}.version.txt
"""
}