mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PANGOLIN {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::pangolin=3.1.11' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1'
|
|
} else {
|
|
container 'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1'
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path('*.csv'), emit: report
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
pangolin \\
|
|
$fasta\\
|
|
--outfile ${prefix}.pangolin.csv \\
|
|
--threads $task.cpus \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(pangolin --version | sed "s/pangolin //g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|