RNAseq_Variant_Calling/tasks/indexBam.wdl

task indexBam {
	File sorted_bam
	String sample
	String base = basename(sorted_bam,'.bam')
	String bam_index = base + ".bam.bai"
	String SAMdocker
	String cluster_config
	String disk_size

	command <<<
		set -o pipefail
		set -e	
		/opt/conda/bin/samtools index ${sorted_bam}
	>>>

	runtime {
		docker:SAMdocker
    	cluster: cluster_config
    	systemDisk: "cloud_ssd 40"
    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File sorted_bam_index = bam_index
	}
}