quartet_dna_quality_control_wgs_big_pipeline/tasks/BQSR.wdl

task BQSR {
	
    File ref_dir
    File dbsnp_dir
    File dbmills_dir
	String fasta
	String dbsnp
	String db_mills
	File realigned_bam
	File realigned_bam_index
	String sample = basename(realigned_bam,".sorted.deduped.realigned.bam")
	String docker
	String cluster_config
	String disk_size

	
	command <<<
		set -o pipefail
		set -e
		gatk BaseRecalibrator \
				-R ${ref_dir}/${fasta} \ 
				-I ${realigned_bam} \
				--known-sites ${dbsnp_dir}/${dbsnp}	\
				--known-sites ${dbmills_dir}/${db_mills} \
				-O ${sample}_recal_data.table
		
		gatk ApplyBQSR \
				-R ${ref_dir}/${fasta} \
				-I ${realigned_bam} \
				-bqsr ${sample}_recal_data.table \
				-O ${sample}.sorted.deduped.realigned.recaled.bam
		
		samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.recaled.bam.bai  ${sample}.sorted.deduped.realigned.recaled.bam
	>>>
	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
	}

	output {
		File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
		File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
	}
}