nf-core_modules/software/seqkit/split2/main.nf

60 lines
1.7 KiB
Text
Raw Normal View History

2021-02-17 16:09:24 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
2021-02-17 16:09:24 +00:00
process SEQKIT_SPLIT2 {
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::seqkit=0.15.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
} else {
container "quay.io/biocontainers/seqkit:0.15.0--0"
}
input:
tuple val(meta), path(reads)
2021-02-17 16:09:24 +00:00
output:
2021-02-23 14:40:22 +00:00
tuple val(meta), path("*.split/*.gz"), emit: reads
2021-02-23 14:00:21 +00:00
path("*.version.txt") , emit: version
2021-02-17 16:09:24 +00:00
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
2021-02-23 13:09:46 +00:00
if(meta.single_end){
2021-02-17 16:09:24 +00:00
"""
seqkit \
split2 \
$options.args \
--threads $task.cpus \
2021-02-23 13:57:07 +00:00
-1 ${reads} \
2021-02-23 14:00:21 +00:00
--out-dir ${prefix}.split
2021-02-17 16:09:24 +00:00
echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
2021-02-23 13:09:46 +00:00
} else {
"""
seqkit \
split2 \
$options.args \
--threads $task.cpus \
-1 ${reads[0]} \
2021-02-23 13:57:07 +00:00
-2 ${reads[1]} \
2021-02-23 14:00:21 +00:00
--out-dir ${prefix}.split
2021-02-23 13:57:07 +00:00
2021-02-23 13:09:46 +00:00
echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
}
2021-02-17 16:09:24 +00:00
}