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18 results

adaptor_removal_single.nf

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  • adaptor_removal_paired.nf 628 B
    log.info "fastq files : ${params.fastq}"
    
    Channel
      .fromFilePairs( params.fastq )
      .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
      .set { fastq_files }
    
    process adaptor_removal {
      tag "$pair_id"
      publishDir "results/fastq/adaptor_removal/", mode: 'copy'
    
      input:
      set pair_id, file(reads) from fastq_files
    
      output:
      set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
    
      script:
      """
      cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
      -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
      ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
      """
    }