nf-core_modules/modules/umitools/extract/main.nf
Harshil Patel 2ade120249
Add --paired flag to umitools dedup and bump to 1.1.2 (#583)
* Add --paired flag to umitools dedup and bump to 1.1.2

* paired not paired_end

* Fix ECLint
2021-07-16 14:21:08 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UMITOOLS_EXTRACT {
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::umi_tools=1.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
} else {
container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
umi_tools \\
extract \\
-I $reads \\
-S ${prefix}.umi_extract.fastq.gz \\
$options.args \\
> ${prefix}.umi_extract.log
echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
"""
} else {
"""
umi_tools \\
extract \\
-I ${reads[0]} \\
--read2-in=${reads[1]} \\
-S ${prefix}.umi_extract_1.fastq.gz \\
--read2-out=${prefix}.umi_extract_2.fastq.gz \\
$options.args \\
> ${prefix}.umi_extract.log
echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
"""
}
}