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Unverified Commit ca35e74a authored by Cats's avatar Cats Committed by GitHub
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Merge pull request #92 from biowdl/BIOWDL-199 

Dockerize GATK. Scattering now works with containers. Tabix another docker image.
parents e55fc372 68ff64af
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biopet/biopet.wdl
+ 20
− 13
View file @ ca35e74a
......@@ -205,54 +205,60 @@ task FastqSync {
task ReorderGlobbedScatters {
input {
Array[File]+ scatters
String scatterDir
# Should not be changed from the main pipeline. As it should not influence results.
String dockerTag = "3.6"
}
command <<<
set -e
# Copy all the scatter files to the CWD so the output matches paths in
# the cwd.
for file in ~{sep=" " scatters}
do cp $file .
done
python << CODE
from os.path import basename
scatters = ['~{sep="','" scatters}']
splitext = [basename(x).split(".") for x in scatters]
splitnum = [x.split("-") + [y] for x,y in splitext]
ordered = sorted(splitnum, key=lambda x: int(x[1]))
merged = ["~{scatterDir}/{}-{}.{}".format(x[0],x[1],x[2]) for x in ordered]
merged = ["{}-{}.{}".format(x[0],x[1],x[2]) for x in ordered]
for x in merged:
print(x)
CODE
>>>
output {
Array[String] reorderedScatters = read_lines(stdout())
Array[File] reorderedScatters = read_lines(stdout())
}
runtime {
memory: 1
docker: "python:" + dockerTag
# 4 gigs of memory to be able to build the docker image in singularity
memory: 4
}
}
task ScatterRegions {
input {
String? preCommand
Reference reference
String outputDirPath
File? toolJar
Int? scatterSize
File? regions
Boolean notSplitContigs = false
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "0.2--0"
}
String toolCommand = if defined(toolJar)
then "java -Xmx" + memory + "G -jar " +toolJar
else "biopet-scatterregions -Xmx" + memory + "G"
# OutDirPath must be defined here because the glob process relies on
# linking. This path must be in the containers filesystem, otherwise the
# linking does not work.
String outputDirPath = "scatters"
command {
set -e -o pipefail
~{preCommand}
mkdir -p ~{outputDirPath}
~{toolCommand} \
biopet-scatterregions -Xmx~{memory}G \
-R ~{reference.fasta} \
-o ~{outputDirPath} \
~{"-s " + scatterSize} \
......@@ -265,6 +271,7 @@ task ScatterRegions {
}
runtime {
docker: "quay.io/biocontainers/biopet-scatterregions:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
......
gatk.wdl
+ 45
− 87
View file @ ca35e74a
......@@ -5,8 +5,6 @@ import "common.wdl"
# Apply Base Quality Score Recalibration (BQSR) model
task ApplyBQSR {
input {
String? preCommand
File? gatkJar
IndexedBamFile inputBam
String outputBamPath
File recalibrationReport
......@@ -15,28 +13,25 @@ task ApplyBQSR {
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
-R ~{reference.fasta} \
-I ~{inputBam.file} \
--use-original-qualities \
-O ~{outputBamPath} \
-bqsr ~{recalibrationReport} \
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
-L ~{sep=" -L " sequenceGroupInterval}
mkdir -p $(dirname ~{outputBamPath})
gatk --java-options -Xmx~{memory}G \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
-R ~{reference.fasta} \
-I ~{inputBam.file} \
--use-original-qualities \
-O ~{outputBamPath} \
-bqsr ~{recalibrationReport} \
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
-L ~{sep=" -L " sequenceGroupInterval}
}
output {
......@@ -48,6 +43,7 @@ task ApplyBQSR {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -55,8 +51,6 @@ task ApplyBQSR {
# Generate Base Quality Score Recalibration (BQSR) model
task BaseRecalibrator {
input {
String? preCommand
File? gatkJar
IndexedBamFile inputBam
String recalibrationReportPath
Array[File]+ sequenceGroupInterval
......@@ -66,6 +60,7 @@ task BaseRecalibrator {
Reference reference
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "4.1.0.0--0"
}
Array[File]+ knownIndelsSitesVCFsArg = flatten([
......@@ -73,14 +68,10 @@ task BaseRecalibrator {
[select_first([dbsnpVCF]).file]
])
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{recalibrationReportPath})
gatk --java-options -Xmx~{memory}G \
BaseRecalibrator \
-R ~{reference.fasta} \
-I ~{inputBam.file} \
......@@ -95,35 +86,28 @@ task BaseRecalibrator {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task CombineGVCFs {
input {
String? preCommand
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File]+ intervals
String outputPath
String? gatkJar
Reference reference
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
CombineGVCFs \
-R ~{reference.fasta} \
-O ~{outputPath} \
......@@ -139,6 +123,7 @@ task CombineGVCFs {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -146,23 +131,18 @@ task CombineGVCFs {
# Combine multiple recalibration tables from scattered BaseRecalibrator runs
task GatherBqsrReports {
input {
String? preCommand
String? gatkJar
Array[File] inputBQSRreports
String outputReportPath
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{outputReportPath})
gatk --java-options -Xmx~{memory}G \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
......@@ -173,39 +153,31 @@ task GatherBqsrReports {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task GenotypeGVCFs {
input {
String? preCommand
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File]+ intervals
String outputPath
String? gatkJar
Reference reference
IndexedVcfFile? dbsnpVCF
Int memory = 6
Float memoryMultiplier = 2.0
String dockerTag = "4.1.0.0--0"
}
File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
GenotypeGVCFs \
-R ~{reference.fasta} \
-O ~{outputPath} \
......@@ -224,7 +196,8 @@ task GenotypeGVCFs {
}
}
runtime{
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -232,31 +205,25 @@ task GenotypeGVCFs {
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
task HaplotypeCallerGvcf {
input {
String? preCommand
Array[File]+ inputBams
Array[File]+ inputBamsIndex
Array[File]+ intervalList
String gvcfPath
Reference reference
Float contamination = 0.0
String? gatkJar
IndexedVcfFile? dbsnpVCF
Int memory = 4
Float memoryMultiplier = 3
String dockerTag = "4.1.0.0--0"
}
File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{gvcfPath})
gatk --java-options -Xmx~{memory}G \
HaplotypeCaller \
-R ~{reference.fasta} \
-O ~{gvcfPath} \
......@@ -275,14 +242,13 @@ task HaplotypeCallerGvcf {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task MuTect2 {
input {
String? preCommand
Array[File]+ inputBams
Array[File]+ inputBamsIndex
Reference reference
......@@ -291,19 +257,15 @@ task MuTect2 {
String? normalSample
Array[File]+ intervals
String? gatkJar
Int memory = 4
Float memoryMultiplier = 3
String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{outputVcf})
gatk --java-options -Xmx~{memory}G \
Mutect2 \
-R ~{reference.fasta} \
-I ~{sep=" -I " inputBams} \
......@@ -321,32 +283,27 @@ task MuTect2 {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task SplitNCigarReads {
input {
String? preCommand
IndexedBamFile inputBam
Reference reference
String outputBam
String? gatkJar
Array[File]+ intervals
Int memory = 4
Float memoryMultiplier = 4
String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
mkdir -p $(dirname ~{outputBam})
gatk --java-options -Xmx~{memory}G \
SplitNCigarReads \
-I ~{inputBam.file} \
-R ~{reference.fasta} \
......@@ -362,6 +319,7 @@ task SplitNCigarReads {
}
runtime {
docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
samtools.wdl
+ 10
− 0
View file @ ca35e74a
......@@ -7,6 +7,7 @@ task BgzipAndIndex {
File inputFile
String outputDir
String type = "vcf"
String dockerTag = "0.2.6--ha92aebf_0"
}
String outputGz = outputDir + "/" + basename(inputFile) + ".gz"
......@@ -20,6 +21,10 @@ task BgzipAndIndex {
File compressed = outputGz
File index = outputGz + ".tbi"
}
runtime {
docker: "quay.io/biocontainers/tabix:" + dockerTag
}
}
task Index {
......@@ -185,6 +190,7 @@ task Tabix {
input {
String inputFile
String type = "vcf"
String dockerTag = "0.2.6--ha92aebf_0"
}
command {
......@@ -194,6 +200,10 @@ task Tabix {
output {
File index = inputFile + ".tbi"
}
runtime {
docker: "quay.io/biocontainers/tabix:" + dockerTag
}
}
task View {
......
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