nf-core_modules/software/shovill/main.nf
Robert A. Petit III 3f14b1fabe
Update shovill module (#337)
* add shovill module

* removed deprecated shovill module

* fix line ending in functions.nf

* fix yaml indentation

* reduce spades memory usage

* update md5sums

* remove non reproducible md5sum

* Update test.yml

Remove last non-reproducible md5sum.

* purely cosmetic order change

* proper process label, improve output readability

Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00

47 lines
1.7 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SHOVILL {
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), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/shovill:1.1.0--0"
} else {
container "quay.io/biocontainers/shovill:1.1.0--0"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("contigs.fa") , emit: contigs
tuple val(meta), path("shovill.corrections") , emit: corrections
tuple val(meta), path("shovill.log") , emit: log
tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
tuple val(meta), path("contigs.{fastg,gfa,LastGraph}") , optional:true, emit: gfa
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def memory = task.memory.toGiga()
"""
shovill \\
--R1 ${reads[0]} \\
--R2 ${reads[1]} \\
$options.args \\
--cpus $task.cpus \\
--ram $memory \\
--outdir ./ \\
--force
echo \$(shovill --version 2>&1) | sed 's/^.*shovill //' > ${software}.version.txt
"""
}