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 """ } stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.html touch ${prefix}.zip cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) END_VERSIONS """ }