daytonapb.nf

#!/usr/bin/env nextflow

/*
Note:
Before running the script, please set the parameters in the config file params.yaml
*/

//Step1:input data files
nextflow.enable.dsl=2
def L001R1Lst = []
def sampleNames = []
myDir = file("$params.input")

myDir.eachFileMatch ~/dem.*.bam/, {L001R1Lst << it.name}
L001R1Lst.sort()
L001R1Lst.each{
   def x = it.minus(".bam")
     //println x
   sampleNames.add(x)

}
//println L001R1Lst
//println sampleNames


//Step2: process the inputed data
A = Channel.fromList(sampleNames)
//A.view()

include { pbsmrtlink } from './modules/pbsmrtlink.nf'
include { moretools } from './modules/moretools.nf'
//include { frag } from './modules/frag.nf'
//include { primer } from './modules/primer.nf'
//include { assembly } from './modules/assembly.nf'
//include { pystats } from './modules/pystats.nf'

workflow {
   pbsmrtlink(A) | moretools | view
}