Skip to content
Snippets Groups Projects
Commit 23dd04d1 authored by Cats's avatar Cats
Browse files

add various CNV calling tasks

parent 5434bc90
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 311 additions and 2 deletions
gatk.wdl
+ 311
− 2
View file @ 23dd04d1
......@@ -251,6 +251,96 @@ task CalculateContamination {
}
}
task CallCopyRatioSegments {
input {
String outputPrefix
File copyRatioSegments
String memory = "21G"
String javaXmx = "6G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(~{outputPrefix})"
gatk --java-options -Xmx~{javaXmx} \
CallCopyRatioSegments \
-I ~{copyRatioSegments} \
-O ~{outputPrefix}.called.seg
}
output {
File calledSegments = outputPrefix + ".called.seg"
File calledSegmentsIgv = outputPrefix + ".called.igv.seg"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
outputPrefix: {description: "The prefix for the output files.", category: "required"}
copyRatioSegments: {description: "The copy ratios file generated by gatk ModelSegments.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CollectAllelicCounts {
input {
String allelicCountsPath = "allelic_counts.tsv"
File commonVariantSites
File inputBam
File inputBamIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
String memory = "90G"
String javaXmx = "30G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(dirname ~{allelicCountsPath})"
gatk --java-options -Xmx~{javaXmx} \
CollectAllelicCounts \
-L ~{commonVariantSites} \
-I ~{inputBam} \
-R ~{referenceFasta} \
-O ~{allelicCountsPath}
}
output {
File allelicCounts = allelicCountsPath
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
allelicCountsPath: {description: "The path the output should be written to.", category: "advanced"}
commonVariantSites: {description: "Interval list of common vairat sies (to retrieve the allelic counts for).", category: "required"}
inputBam: {description: "The BAM file to generate counts for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CollectReadCounts {
input {
String countsPath = "readcounts.hdf5"
......@@ -290,7 +380,7 @@ task CollectReadCounts {
}
parameter_meta {
countsPath: {description: "The location the output should be written to.", category: "required"}
countsPath: {description: "The location the output should be written to.", category: "advanced"}
intervals: {description: "The intervals to collect counts for.", category: "required"}
inputBam: {description: "The BAM file to determine the coverage for.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
......@@ -463,7 +553,7 @@ task CreateReadCountPanelOfNormals {
parameter_meta {
PONpath: {description: "The location the PON should be written to.", category: "common"}
readCountsFiles: {description: "The read counts files as generated by CollectReadCounts.", category: "advanced"}
readCountsFiles: {description: "The read counts files as generated by CollectReadCounts.", category: "required"}
annotatedIntervals: {description: "An annotation set of intervals as generated by AnnotateIntervals. If provided, explicit GC correction will be performed.",
category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
......@@ -474,6 +564,54 @@ task CreateReadCountPanelOfNormals {
}
}
task DenoiseReadCounts {
input {
File? PON
File? annotatedIntervals
File readCounts
String outputPrefix
String memory = "39G"
String javaXmx = "13G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
gatk --java-options -Xmx~{javaXmx} \
DenoiseReadCounts \
-I ~{readCounts} \
~{"--count-panel-of-normals " + PON} \
~{"--annotated-intervals " + annotatedIntervals} \
--standardized-copy-ratios ~{outputPrefix}.standardizedCR.tsv \
--denoised-copy-ratios ~{outputPrefix}.denoisedCR.tsv
}
output {
File standardizedCopyRatios = outputPrefix + ".standardizedCR.tsv"
File denoisedCopyRatios = outputPrefix + ".denoisedCR.tsv"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
PON: {description: "A panel of normals as generated by CreateReadCountPanelOfNormals.", category: "advanced"}
annotatedIntervals: {description: "An annotated set of intervals as generated by AnnotateIntervals. Will be ignored if PON is provided.",
category: "advanced"}
readCounts: {description: "The read counts file as generated by CollectReadCounts.", category: "required"}
outputPrefix: {description: "The prefix for the output files.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task FilterMutectCalls {
input {
File referenceFasta
......@@ -836,6 +974,73 @@ task MergeStats {
}
}
task ModelSegments {
input {
String outputDir = "."
String outputPrefix
File denoisedCopyRatios
File allelicCounts
File? normalAllelicCounts
Int minimumTotalAlleleCountCase = if defined(normalAllelicCounts)
then 0
else 30
Int maximumNumberOfSmoothingIterations = 10
String memory = "64G"
String javaXmx = "10G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p ~{outputDir}
gatk --java-options -Xmx~{javaXmx} \
ModelSegments \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
~{"--normal-allelic-counts " + normalAllelicCounts} \
--minimum-total-allele-count-case ~{minimumTotalAlleleCountCase}
--maximum-number-of-smoothing-iterations ~{maximumNumberOfSmoothingIterations}
--output ~{outputDir} \
--output-prefix ~{outputPrefix}
}
output {
File hetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.tsv"
File normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
File copyRatioSegments = outputDir + "/" + outputPrefix + ".cr.seg"
File copyRatioCBS = outputDir + "/" + outputPrefix + ".cr.igv.seg"
File alleleFractionCBS = outputDir + "/" + outputPrefix + ".af.igv.seg"
File unsmoothedModeledSegments = outputDir + "/" + outputPrefix + ".modelBegin.seg"
File unsmoothedCopyRatioParameters = outputDir + "/" + outputPrefix + ".modelBegin.cr.param"
File unsmoothedAlleleFractionParameters = outputDir + "/" + outputPrefix + ".modelBegin.af.param"
File modeledSegments = outputDir + "/" + outputPrefix + ".modelFinal.seg"
File copyRatioParameters = outputDir + "/" + outputPrefix + ".modelFinal.cr.param"
File alleleFractionParameters = outputDir + "/" + outputPrefix + ".modelFinal.af.param"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
allelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts.", category: "required" }
normalAllelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts for a matched normal.", category: "common"}
minimumTotalAlleleCountCase: {description: "Equivalent to gatk ModelSeqments' `--minimum-total-allele-count-case` option.", category: "advanced"}
maximumNumberOfSmoothingIterations: {description: "Equivalent to gatk ModelSeqments' `--maximum-number-of-smoothing-iterations` option.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task MuTect2 {
input {
Array[File]+ inputBams
......@@ -911,6 +1116,110 @@ task MuTect2 {
}
}
task PlotDenoisedCopyRatios {
input {
File referenceFastaDict
String outputDir = "."
String outputPrefix
File standardizedCopyRatios
File denoisedCopyRatios
String memory = "21G"
String javaXmx = "7G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p ~{outputDir}
gatk --java-options -XmX~{javaXmx} \
PlotDenoisedCopyRatios \
--standardized-copy-ratios ~{standardizedCopyRatios} \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--sequence-dictionary ~{referenceFastaDict} \
--output ~{outputDir} \
--output-prefix ~{outputPrefix}
}
output {
File denoisedCopyRatiosPlot = outputDir + "/" + outputPrefix + ".denoised.png"
File denoisedCopyRatiosLimitedPlot = outputDir + "/" + outputPrefix + ".denoisedLimit4.png"
File standardizedMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".standardizedMAD.txt"
File denoisedMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".denoisedMAD.txt"
File deltaMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".deltaMAD.txt"
File deltaScaledMedianAbsoluteDeviation = outputDir + "/" + outputPrefix + ".scaledDeltaMAD.txt"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file used for the analyses.", category: "required"}
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
standardizedCopyRatios: {description: "The standardized copy ratios as generated by DenoiseReadCounts.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task PlotModeledSegments {
input {
File referenceFastaDict
String outputDir = "."
String outputPrefix
File denoisedCopyRatios
File segments
File allelicCounts
String memory = "21G"
String javaXmx = "7G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p ~{outputDir}
gatk --java-option -Xmx~{javaXmx} \
PlotModeledSegments \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
--segments ~{segments} \
--sequence-dictionary ~{referenceFastaDict} \
--output ~{outputDir} \
--output-prefix ~{outputPrefix}
}
output {
File modeledSegmentsPlot = outputDir + "/" + outputPrefix + ".modeled.png"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file used for the analyses.", category: "required"}
outputDir: {description: "The directory to write the ouput to.", category: "common"}
outputPrefix: {description: "The prefix of the output files. Should not include directories.", category: "required"}
denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
segments: {description: "The modeled segments as generated by ModelSegments.", category: "required"}
allelicCounts: {description: "The hetrozygous allelic counts as generated by ModelSegments.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task PreprocessIntervals {
input {
File referenceFasta
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment