mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
def VERSION = '2.3.2' // Version information not provided by tool on CLI
|
|
|
|
process RAPIDNJ {
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' :
|
|
'quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' }"
|
|
|
|
input:
|
|
path alignment
|
|
|
|
output:
|
|
path "*.sth" , emit: stockholm_alignment
|
|
path "*.tre" , emit: phylogeny
|
|
path "versions.yml", emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
python \\
|
|
-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
|
|
|
|
rapidnj \\
|
|
alignment.sth \\
|
|
$args \\
|
|
-i sth \\
|
|
-c $task.cpus \\
|
|
-x rapidnj_phylogeny.tre
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
rapidnj: $VERSION
|
|
biopython: \$(python -c "import Bio; print(Bio.__version__)")
|
|
END_VERSIONS
|
|
"""
|
|
}
|