mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
45 lines
1.3 KiB
Text
45 lines
1.3 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
params.options = [:]
|
||
|
|
def options = initOptions(params.options)
|
||
|
|
|
||
|
|
def VERSION = '0.4.1'
|
||
|
|
|
||
|
|
process SEQWISH_INDUCE {
|
||
|
|
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::seqwish=0.4.1" : null)
|
||
|
|
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(paf), path(fasta)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.gfa"), emit: gfa
|
||
|
|
path "*.version.txt" , emit: version
|
||
|
|
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
"""
|
||
|
|
seqwish \\
|
||
|
|
--threads $task.cpus \\
|
||
|
|
--paf-alns=$paf \\
|
||
|
|
--seqs=$fasta \\
|
||
|
|
--gfa=${prefix}.gfa \\
|
||
|
|
$options.args
|
||
|
|
|
||
|
|
echo $VERSION > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|