quartet_dna_quality_control_wes_big_pipeline/tasks/Realigner.wdl

task Realigner {

    File ref_dir
    File dbmills_dir

	String fasta

	File Dedup_bam
	File Dedup_bam_index
	String sample = basename(Dedup_bam,".sorted.deduped.bam")
	String db_mills
	String docker	
	String cluster_config
	String disk_size


	command <<<
	set -o pipefail
	set -e
	nt=$(nproc)
	/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ${ref_dir}/${fasta} -nt $nt -I ${Dedup_bam} -known ${dbmills_dir}/${db_mills} -o ${sample}.IndelRealigner.intervals
	/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T IndelRealigner -R ${ref_dir}/${fasta} -I ${Dedup_bam} --targetIntervals ${sample}.IndelRealigner.intervals -o ${sample}.sorted.deduped.realigned.bam
	/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.bam.bai  ${sample}.sorted.deduped.realigned.bam
	>>>

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

	output {
		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"

	}
}