import "./tasks/hisat2.wdl" as hisat2
import "./tasks/samtools.wdl" as samtools
import "./tasks/stringtie.wdl" as stringtie
import "./tasks/ballgown.wdl" as ballgown

workflow {{ project_name }} {

	File read1
	File read2
    File idx
	String idx_prefix
    File gtf
	
	
	call hisat2.hisat2 as hisat2 {
		input: idx=idx, idx_prefix=idx_prefix, read_1P=read1, read_2P=read2
	}

    all samtools.samtools as samtools {
        input: sam = hisat2.sam
	}

    call stringtie.stringtie as stringtie {
        input: gtf = gtf, bam = samtools.out_bam
	}   

	call ballgown.ballgown as ballgown {
		input: ballgown = stringtie.ballgown
	}

        
	
}