nf-core_modules/modules/rapidnj/main.nf

49 lines
1.7 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '2.3.2' // No version information printed
process RAPIDNJ {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
} else {
container "quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
}
input:
path alignment
output:
path "*.sth" , emit: stockholm_alignment
path "*.tre" , emit: phylogeny
path "versions.yml", emit: versions
script:
"""
python \\
-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
rapidnj \\
alignment.sth \\
$options.args \\
-i sth \\
-c $task.cpus \\
-x rapidnj_phylogeny.tre
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo $VERSION)
biopython: \$(python -c "import Bio; print(Bio.__version__)")
END_VERSIONS
"""
}