import "./tasks/delly.wdl" as delly
import "./tasks/AnnotSV.wdl" as AnnotSV
import "./tasks/MSIsensor.wdl" as MSIsensor

workflow {{ project_name }}{
    String sample_id
    File ref_fasta_dir
    String ref_fasta
    File sample_tsv
    File tumor_bam
    File tumor_bam_bai
    File normal_bam
    File normal_bam_bai
    String docker_delly
    String cluster_config
    String disk_size
    File annotsv_database
    File baseline
    String docker_annotsv
    String docker_MSIsensor

    call delly.delly as delly{
        input:
            sample=sample_id,
            ref_dir=ref_fasta_dir,
            fasta=ref_fasta,
            sample_tsv=sample_tsv,
            tumor_bam=tumor_bam,
            tumor_bam_index=tumor_bam_bai,
            normal_bam=normal_bam,
            normal_bam_index=normal_bam_bai,
            docker=docker_delly,
            cluster_config=cluster_config,
            disk_size=disk_size

    }

    call MSIsensor.MSIsensor as MSIsensor{
        input:
            sample = sample_id,
            ref_dir = ref_fasta_dir,
            fasta = ref_fasta,
            tumor_bam=tumor_bam,
            tumor_bam_index =tumor_bam_bai,
            normal_bam = normal_bam,
            normal_bam_index=normal_bam_bai,
            baseline=baseline,
            docker = docker_MSIsensor,
            cluster_config = cluster_config,
            disk_size = disk_size
    }

	call AnnotSV.AnnotSV as delly_AnnotSV{
		input:
                sample=sample_id,
                somatic_vcf= delly.pass_vcf,
                annotsv_database=annotsv_database,
                docker=docker_annotsv,
                cluster_config=cluster_config,
                disk_size=disk_size
		
	}
}