import "./tasks/pathseq.wdl" as pathseq

workflow {{ project_name }} {
    String sample_id
    File fastq1
    File fastq2
    String disk_size
   
    File host_image
    File host_kmer
    File microbe_dict
    File microbe_bwa_image
    File microbe_taxonomy

    String pathseq_docker
    String pathseq_cluster



        call pathseq.pathseq as pathseq {
                input:
                sample_id=sample_id,
                fastq1=fastq1,
                fastq2=fastq2,
                host_image=host_image,
                host_kmer=host_kmer,
                microbe_dict=microbe_dict,
                microbe_bwa_image=microbe_bwa_image,
                microbe_taxonomy=microbe_taxonomy,
                disk_size=disk_size,
                docker=pathseq_docker,
                cluster=pathseq_cluster
        }



}