nf-core_modules/software/fastqc/main.nf

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