import "./tasks/replicate_consensus.wdl" as replicate_consensus import "./tasks/mendelian.wdl" as mendelian import "./tasks/filtered_benchmark.wdl" as filtered_benchmark import "./tasks/merge_mendelian.wdl" as merge_mendelian workflow {{ project_name }} { File ref_dir File LCL5_info_dir File LCL5_benchmark_call File chromo_file String fasta String chromo String cluster_config String disk_size call replicate_consensus.replicate_consensus as replicate_consensus { input: chromo_file=chromo_file, chromo=chromo, cluster_config=cluster_config, disk_size=disk_size } call mendelian.mendelian as mendelian { input: consensus_vcf=replicate_consensus.consensus_vcf, ref_dir=ref_dir, fasta=fasta, chromo=chromo, cluster_config=cluster_config, disk_size=disk_size } call filtered_benchmark.filtered_benchmark as filtered_benchmark { input: chromo_consensus=replicate_consensus.chromo_consensus, LCL5_info_dir=LCL5_info_dir, LCL5_benchmark_call=LCL5_benchmark_call, chromo=chromo, cluster_config=cluster_config, disk_size=disk_size } call merge_mendelian.merge_mendelian as merge_mendelian { input: D5_trio_vcf=mendelian.D5_trio_vcf, D6_trio_vcf=mendelian.D6_trio_vcf, consensus_vcf=replicate_consensus.consensus_vcf, chromo=chromo, cluster_config=cluster_config, disk_size=disk_size } }