nf-core_modules/modules/pangolin/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

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
"""
}