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main.nf

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  • main.nf 735 B
    version = "0.11.5"
    container_url = "lbmc/fastqc:${version}"
    
    params.fastqc_fastq = ""
    params.fastqc_fastq_out = ""
    process fastqc_fastq {
      container = "${container_url}"
      label "big_mem_mono_cpus"
      tag "$file_id"
      if (params.fastqc_fastq_out != "") {
        publishDir "results/${params.fastqc_fastq_out}", mode: 'copy'
      }
    
      input:
      tuple val(file_id), path(reads)
    
      output:
      tuple val(file_id), path("*.{zip,html}"), emit: report
    
      script:
      if (reads.size() == 2)
      """
      fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
        ${params.fastqc_fastq} \
        ${reads[0]} ${reads[1]}
      """
      else
      """
        fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${params.fastqc_fastq} ${reads[0]}
      """
    }