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cram-to-bam-old.wdl
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cram-to-bam-old.wdl
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## Copyright Broad Institute, 2017
## This script should convert a CRAM to SAM to BAM and output a BAM, BAM Index, and validation report to a Google bucket. If you'd like to do ## this on multiple CRAMS, create a sample set in the Data tab.
## The reason this approach was chosen instead of converting CRAM to BAM directly using Samtools is because Samtools 1.3 produces incorrect
## bins due to an old version of htslib included in the package. Samtools versions 1.4 & 1.5 have an NM issue that causes them to not validate ## with Picard.
##
## TESTED: It was tested using the Genomes in the Cloud Docker image version 2.3.1-1500064817.
## Versions of other tools on this image at the time of testing:
## PICARD_VER=1.1150
## GATK34_VER=3.4-g3c929b0
## GATK35_VER=3.5-0-g36282e4
## GATK36_VER=3.6-44-ge7d1cd2
## GATK4_VER=4.beta.1
## SAMTOOLS_VER=1.3.1
## BWA_VER=0.7.15.r1140
## TABIX_VER=0.2.5_r1005
## BGZIP_VER=1.3
## SVTOOLKIT_VER=2.00-1650
## It was tested pulling the HG38 reference Fasta and Fai.
## Successfully tested on Cromwell version 28. Does not work on versions < v23 due to output syntax
## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
##
## 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 for detailed licensing information pertaining to the included programs.
##
#WORKFLOW DEFINITION
workflow CramToBamFlow {
Int cram_to_bam_disk_size
Int validate_sam_file_disk_size
String cram_to_bam_mem_size
String validate_sam_file_mem_size
String sample_name
String? gotc_docker_override
String gotc_docker = select_first([gotc_docker_override, "broadinstitute/genomes-in-the-cloud:2.3.1-1500064817"])
File RefFasta
File RefIndex
File RefDict
File InputCram
#converts CRAM to SAM to BAM and makes BAI
call CramToBamTask{
input:
disk_size = cram_to_bam_disk_size,
mem_size = cram_to_bam_mem_size,
docker_image = gotc_docker,
SampleName = sample_name,
RefFasta = RefFasta,
RefIndex = RefIndex,
RefDict = RefDict,
InputCram = InputCram
}
#validates Bam
call ValidateSamFile{
input:
input_bam = CramToBamTask.outputBam,
disk_size = validate_sam_file_disk_size,
mem_size = validate_sam_file_mem_size,
docker_image = gotc_docker
}
#Outputs Bam, Bai, and validation report to the FireCloud data model
output {
File outputBam = CramToBamTask.outputBam
File outputBai = CramToBamTask.outputBai
File validation_report = ValidateSamFile.report
}
}
#Task Definitions
task CramToBamTask {
File RefFasta
File RefIndex
File RefDict
File InputCram
#File InputCrai
String SampleName
Int disk_size
String mem_size
String docker_image
#Calls samtools view to do the conversion
command {
#Set -e and -o says if any command I run fails in this script, make sure to return a failure
#Changed to check that the input is a Cram, otherwise if it is a Bam, it does not do a conversion,
#or if it is neither, it returns an error.
set -e
set -o pipefail
if [[ "`basename ${InputCram} | sed 's/.*\.//'`" = "cram" ]]; then
samtools view -@ 2 -h -T ${RefFasta} ${InputCram} | samtools view -@ 2 -b -o ${SampleName}.bam -
elif [[ "`basename ${InputCram} | sed 's/.*\.//'`" = "bam" ]]; then
mv ${InputCram} ${SampleName}.bam
else
exit 1
fi
#Change to correct sample name (since external sequencing will have a different sample name)
samtools view -H ${SampleName}.bam | sed "s/SM:[^\t]*/SM:${SampleName}/g" | samtools reheader - ${SampleName}.bam > ${SampleName}_SM.bam
mv ${SampleName}_SM.bam ${SampleName}.bam
samtools index -b ${SampleName}.bam
mv ${SampleName}.bam.bai ${SampleName}.bai
}
#Run time attributes:
#Use a docker with samtools. Set this up as a workspace attribute.
#cpu of one because no multi-threading is required. This is also default, so don't need to specify.
#disk_size should equal input size + output size + buffer
runtime {
#docker: docker_image
docker: "halllab/samtools:v1.9"
memory: mem_size
cpu: "4"
disks: "local-disk " + disk_size + " HDD"
}
#Outputs a BAM and BAI with the same sample name
output {
File outputBam = "${SampleName}.bam"
File outputBai = "${SampleName}.bai"
}
}
#Validates BAM output to ensure it wasn't corrupted during the file conversion
task ValidateSamFile {
File input_bam
String output_name = basename(input_bam, ".bam") + ".validation_report"
Int disk_size
String mem_size
Int preemptible_tries
String docker_image
command {
java -Xmx3000m -jar /usr/gitc/picard.jar \
ValidateSamFile \
INPUT=${input_bam} \
OUTPUT=${output_name} \
MODE=SUMMARY \
IS_BISULFITE_SEQUENCED=false
}
#Run time attributes:
#Use a docker with the picard.jar. Set this up as a workspace attribute.
#Read more about return codes here: https://github.com/broadinstitute/cromwell#continueonreturncode
runtime {
docker: docker_image
memory: mem_size
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
continueOnReturnCode: [0,1]
}
#A text file is generated that will list errors or warnings that apply.
output {
File report = "${output_name}"
}
}