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Laurent Modolo authoredLaurent Modolo authored
fastqc_single.nf 526 B
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process fastqc_fastq {
tag "$reads.baseName"
publishDir "results/fastq/fastqc/", mode: 'copy'
cpus = 1
input:
file reads from fastq_files
output:
file "*.{zip,html}" into fastqc_report
script:
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
"""
}