nextflow.enable.dsl=2

/*
Testing pipeline for marseq scRNASeq analysis
*/

include { KMC } from "./modules/kmc.nf"


Channel.fromPath( file(params.csv) )
                    .splitCsv(header: true)
                    .multiMap{row ->
                        fastq_r1 = file("${row.r1}")
                        fastq_r2 = file("${row.r2}")
                        r1: [['id': fastq_r1.simpleName, 'specie': row.specie, 'sex': row.sex, 'read': 'r1'], fastq_r1]
                        r2: [['id': fastq_r1.simpleName, 'specie': row.specie, 'sex': row.sex, 'read': 'r2'], fastq_r2]
                    }
                    .set{ fastq }

workflow {
  KMC(fastq.r1.mix(fastq.r2))
}