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version = "0.11.5"
container_url = "lbmc/fastqc:${version}"
process fastqc_fastq_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
publishDir "results/fastq/fastqc/", mode: 'copy'
input:
tuple val(pair_id), path(reads)
output:
path "*.{zip,html}", emit: report
script:
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
${reads[0]} ${reads[1]}
"""
}
process fastqc_fastq_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
publishDir "results/fastq/fastqc/", mode: 'copy'
input:
tuple val(file_id), path(reads)
output:
path "*.{zip,html}", emit: report
script:
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
"""
}