main.nf

nextflow.enable.dsl=2

include { FASTQC } from './modules/fastqc.nf' 
include { MULTIQC } from './modules/multiqc.nf' 


// this prevents a warning of undefined parameter
params.help             = false
params.input_dir        = ''
params.output_dir       = ''


// this prints the input parameters
log.info """
         BASIC FASTQ FILE QC - N F   P I P E L I N E 
        ============================================
         input_reads_path        : ${params.input_dir}
         output_dir              : ${params.output_dir}
"""

// this prints the help in case you use --help parameter in the command line and it stops the pipeline

if (params.help) {
    log.info 'This is BASIC FASTQ FILE QC Pipeline\n'
    log.info 'Please define input_reads_path and output_dir!\n'
    log.info '\n'
    exit 1
}
      

workflow {
  
  reads_ch = Channel.fromFilePairs("$params.input_dir/*{1,2}.fastq.gz")
  
  fastqc_ch = FASTQC(reads_ch)
  
  MULTIQC(fastqc_ch)
  
}

workflow.onComplete {

    println ( workflow.success ? """
        Pipeline execution summary
        ---------------------------
        Completed at: ${workflow.complete}
        Duration    : ${workflow.duration}
        Success     : ${workflow.success}
        workDir     : ${workflow.workDir}
        exit status : ${workflow.exitStatus}
        """ : """
        Failed: ${workflow.errorReport}
        exit status : ${workflow.exitStatus}
        """
    )
}