mendelian_vote_summary/tasks/merge_mendelian_vote.wdl

task merge_mendelian_vote {
	File vote_file
	File mendelian_file
	File mut_file
	String output_prefix
	String docker
	String cluster_config
	String disk_size
	
	command <<<

		python /opt/merge_mendelian_vote.py ${mendelian_file} ${vote_file} ${mut_file} ${output_prefix}.mendelian.vote.txt

		cat ${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) == 1) && (length($7) == 1)) { print } }' > ${output_prefix}.snv

		cat ${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) > 1) || (length($7) > 1)) { print } }' > ${output_prefix}.indel		

	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File mendelian_vote = "${output_prefix}.mendelian.vote.txt"
		File mendelian_vote_snv = "${output_prefix}.snv"
		File mendelian_vote_indel = "${output_prefix}.indel"
	}
}