RNAseq_Variant_Calling/tasks/deduped_Metrics.wdl

task deduped_Metrics {

    File ref_dir
    
	String SENTIEON_INSTALL_DIR
	String sample
	String fasta
	File Dedup_bam
	File Dedup_bam_index
	String docker
	String cluster_config
	String disk_size


	command <<<
		set -o pipefail
		set -e
		export SENTIEON_LICENSE=192.168.0.55:8990
		nt=$(nproc)
		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --traverse_param 1000000/10000 -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} \
		--algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics \
		--algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt \
		--algo QualDistribution ${sample}_deduped_qd_metrics.txt \
		--algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt \
		--algo AlignmentStat ${sample}_deduped_aln_metrics.txt \
		--algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt
	>>>

	runtime {
		docker:docker
    	cluster: cluster_config
    	systemDisk: "cloud_ssd 40"
    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
	}

	output {
		File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
		File deduped_mq_metrics = "${sample}_deduped_mq_metrics.txt"
		File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
		File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
		File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
		File deduped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
		File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
		File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
		File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
		File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
		File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
	}
}