mendelian_vote_summary/tasks/merge_chromo.wdl

task merge_chromo {
	Array[File] mendelian_vote_snv
	Array[File] mendelian_vote_indel
	String sample_name
	String docker
	String cluster_config
	String disk_size
	
	command <<<

		cat ${sep=" " mendelian_vote_snv} > ${sample_name}.snv.txt

		cat ${sep=" " mendelian_vote_indel} > ${sample_name}.indel.txt

		cat ${sample_name}.snv.txt |  cut -f3,4 | sort | uniq -c > ${sample_name}.snv.summary.txt

		cat ${sample_name}.indel.txt |  cut -f3,4 | sort | uniq -c > ${sample_name}.indel.summary.txt

	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File mendelian_vote_summary_snv = "${sample_name}.snv.summary.txt"
		File mendelian_vote_summary_indel = "${sample_name}.indel.summary.txt"
		File mendelian_vote_summary_snv_detail = "${sample_name}.snv.txt"
		File mendelian_vote_summary_indel_detail = "${sample_name}.indel.txt"
	}
}