nf-core_modules/modules/qcat/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process QCAT {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0"
} else {
container "quay.io/biocontainers/qcat:1.1.0--py_0"
}
input:
tuple val(meta), path(reads)
val barcode_kit
output:
tuple val(meta), path("fastq/*.fastq.gz"), emit: reads
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
## Unzip fastq file
## qcat doesn't support zipped files yet
FILE=$reads
if [[ \$FILE == *.gz ]]
then
zcat $reads > unzipped.fastq
FILE=unzipped.fastq
fi
qcat \\
-f \$FILE \\
-b ./fastq \\
--kit $barcode_kit
## Zip fastq files
gzip fastq/*
echo \$(qcat --version 2>&1) | sed 's/^.*qcat //; s/ .*\$//' > ${software}.version.txt
"""
}