import "./tasks/mendelian.wdl" as mendelian import "./tasks/merge.wdl" as merge import "./tasks/KeepVar.wdl" as KeepVar workflow {{ project_name }} { File inputSamplesFile Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) File sdf String cluster_config String disk_size scatter (sample in inputSamples){ call mendelian.mendelian as mendelian { input: mother_vcf_gz=sample[0], father_vcf_gz=sample[1], child_vcf_gz=sample[2], mother_vcf_idx=sample[3], father_vcf_idx=sample[4], child_vcf_idx=sample[5], mother_name=sample[6], father_name=sample[7], child_name=sample[8], family_name=sample[9], sdf=sdf, cluster_config=cluster_config, disk_size=disk_size } } call merge.merge as merge { input: violation_vcf_gz=mendelian.violation_vcf_gz, violation_vcf_idx=mendelian.violation_vcf_idx, consistent_vcf_gz=mendelian.consistent_vcf_gz, consistent_vcf_idx=mendelian.consistent_vcf_idx, cluster_config=cluster_config, disk_size=disk_size } call KeepVar.KeepVar as KeepVar { input: violation_merged_vcf=merge.violation_merged_vcf, consistent_merged_vcf=merge.consistent_merged_vcf, cluster_config=cluster_config, disk_size=disk_size } }