nf-core_modules/software/rasusa/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

43 lines
1.5 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process RASUSA {
tag "$meta.id"
label 'process_low'
publishDir "${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::rasusa=0.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1"
} else {
container "quay.io/biocontainers/rasusa:0.3.0--h779adbc_1"
}
input:
tuple val(meta), path(reads)
val depth_cutoff
val genome_size
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def output = meta.single_end ? "--output ${prefix}.fastq.gz" : "--output ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz"
"""
rasusa \\
$options.args \\
--coverage $depth_cutoff \\
--genome-size $genome_size \\
--input $reads \\
$output
echo \$(rasusa --version 2>&1) | sed -e "s/rasusa //g" > ${software}.version.txt
"""
}