version 1.0
## Copyright Broad Institute, 2018
##
## This WDL converts BAM  to unmapped BAMs
##
## Requirements/expectations :
## - BAM file
##
## Outputs :
## - Sorted Unmapped BAMs
##
## Cromwell version support
## - Successfully tested on v47
## - Does not work on versions < v23 due to output syntax
##
## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
## For program versions, see docker containers.
##
## LICENSING :
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
## be subject to different licenses. Users are responsible for checking that they are
## authorized to run all programs before running this script. Please see the docker
## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed
## licensing information pertaining to the included programs.

# WORKFLOW DEFINITION
workflow BamToUnmappedBams {
	input {
		File input_bam

		Int additional_disk_size = 20
		String gatk_docker = "public.ecr.aws/aws-genomics/broadinstitute/gatk:4.1.9.0"
		String gatk_path = "/gatk/gatk"
	}

	call RevertSam {
		input:
			input_bam = input_bam,
			docker = gatk_docker,
			gatk_path = gatk_path
	}

	scatter (unmapped_bam in RevertSam.unmapped_bams) {
		String output_basename = basename(unmapped_bam, ".coord.sorted.unmapped.bam")

		call SortSam {
			input:
				input_bam = unmapped_bam,
				sorted_bam_name = output_basename + ".unmapped.bam",
				docker = gatk_docker,
				gatk_path = gatk_path
		}
	}

	output {
		Array[File] output_bams = SortSam.sorted_bam
	}
}

task RevertSam {
	input {
		#Command parameters
		File input_bam
		String gatk_path

		#Runtime parameters
		String docker
		Int machine_mem_gb = 2
		Int preemptible_attempts = 3
		Int awsBatchRetryAttempts = 3
	}
	Int command_mem_gb = machine_mem_gb - 1    ####Needs to occur after machine_mem_gb is set

	command {

		~{gatk_path} --java-options "-Xmx~{command_mem_gb}g" \
		RevertSam \
		--INPUT ~{input_bam} \
		--OUTPUT ./ \
		--OUTPUT_BY_READGROUP true \
		--VALIDATION_STRINGENCY LENIENT \
		--ATTRIBUTE_TO_CLEAR FT \
		--ATTRIBUTE_TO_CLEAR CO \
		--SORT_ORDER coordinate
	}
	runtime {
		docker: docker
		memory: machine_mem_gb + " GB"
		preemptible: preemptible_attempts
		awsBatchRetryAttempts: awsBatchRetryAttempts
	}
	output {
		Array[File] unmapped_bams = glob("*.bam")
	}
}

task SortSam {
	input {
		#Command parameters
		File input_bam
		String sorted_bam_name
		#Runtime parameters
		String gatk_path
		String docker
		Int machine_mem_gb = 4
		Int preemptible_attempts = 3
		Int awsBatchRetryAttempts = 3
	}
	Int command_mem_gb = machine_mem_gb - 1    ####Needs to occur after machine_mem_gb is set

	command {
		~{gatk_path} --java-options "-Xmx~{command_mem_gb}g" \
		SortSam \
		--INPUT ~{input_bam} \
		--OUTPUT ~{sorted_bam_name} \
		--SORT_ORDER queryname \
		--MAX_RECORDS_IN_RAM 1000000
	}
	runtime {
		docker: docker
		memory: machine_mem_gb + " GB"
		preemptible: preemptible_attempts
		awsBatchRetryAttempts: awsBatchRetryAttempts
	}
	output {
		File sorted_bam = "~{sorted_bam_name}"
	}
}