main.nf

nextflow.enable.dsl=2

include { validateParameters; paramsHelp; paramsSummaryLog; samplesheetToList } from 'plugin/nf-schema'

// Print help message, supply typical command line usage for the pipeline
if (params.help) {
   log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
   exit 0
}

// Validate input parameters
// TODO validateParameters()

// Print summary of supplied parameters
log.info paramsSummaryLog(workflow)

// Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))


include { PRIMER3 } from './subworkflows/primer3'

workflow {
  // Read in bed file(s)
  // Pull raw sequences in the bed files from the reference genome
  // Run primer3 on the sequences
  PRIMER3 (
    Channel.of(params.targetseq),
    Channel.fromPath(params.fasta),
  )
}