nf-core_modules/software/fastqc/main.nf
2020-08-05 17:17:58 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process FASTQC {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/fastqc:0.11.9--0"
//container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
conda (params.conda ? "bioconda::fastqc=0.11.9" : null)
input:
tuple val(meta), path(reads)
val options
output:
tuple val(meta), path("*.html"), emit: html
tuple val(meta), path("*.zip"), emit: zip
path "*.version.txt", emit: version
script:
// Add soft-links to original FastQs for consistent naming in pipeline
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
def prefix = ioptions.suffix ? "${meta.id}.${ioptions.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
fastqc $ioptions.args --threads $task.cpus ${prefix}.fastq.gz
fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
"""
} else {
"""
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
fastqc $ioptions.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
"""
}
}