mendelian_vote_summary/workflow.wdl

import "./tasks/merge_mendelian_vote.wdl" as merge_mendelian_vote
import "./tasks/summary_mendelian.wdl" as summary_mendelian
import "./tasks/merge_chromo.wdl" as merge_chromo

workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	String docker
	String sample_name
	String cluster_config
	String disk_size

	scatter (sample in inputSamples){
		call merge_mendelian_vote.merge_mendelian_vote as merge_mendelian_vote {
			input:
			vote_file=sample[0],
			mendelian_file=sample[1],
			output_prefix=sample[2],
			docker=docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call summary_mendelian.summary_mendelian as summary_mendelian {
			input:
			mendelian_vote=merge_mendelian_vote.mendelian_vote,
			output_prefix=sample[2],
			docker=docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}
	call merge_chromo.merge_chromo as merge_chromo {
		input:
		mendelian_vote_summary=summary_mendelian.mendelian_vote_summary,
		sample_name=sample_name,
		docker=docker,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
}