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

workflow {{ project_name }} {

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

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

        call arcashla.arcashla as arcashla {
            input: 
			bam = samtools.out_bam,
			disk_size=disk_size,
		    cluster_config=cluster_config
	}
        
	
}