nf-core_modules/modules/fastqc/main.nf
2022-02-04 09:53:32 +01:00

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process FASTQC {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
'quay.io/biocontainers/fastqc:0.11.9--0' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.html"), emit: html
tuple val(meta), path("*.zip") , emit: zip
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
// Add soft-links to original FastQs for consistent naming in pipeline
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
fastqc $args --threads $task.cpus ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
} 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 $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
}
}