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

workflow {{ project_name }} {

	File read1
	File read2
    File idx
	String idx_prefix
    File anno_gtf
	String sample_id
	
	
	call hisat2.hisat2 as hisat2 {
		input: 
		idx=idx, 
		idx_prefix=idx_prefix, 
		read1=read1,
		read2=read2,
		sample_id=sample_id
	}

    call samtools.samtools as samtools {
        input: 
		sample_id=sample_id, 
		sam = hisat2.sam
	}

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