diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index e8884ab01a0b82f1829dd4223fe30a60f0c6129d..1b911dbbcc45b4b50d0c7f866088841c46c43b10 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -37,18 +37,18 @@ task Bam2Fasta {
command {
set -e
- mkdir -p "$(dirname ~{outputPrefix})"'
+ mkdir -p "$(dirname ~{outputPrefix})"
# Localise the bam and pbi files so they are next to each other in the
# current folder.
bamFiles=""
- for bamFile in ~{sep=" " bam};
+ for bamFile in ~{sep=" " bam}
do
ln ${bamFile} .
bamFiles=${bamFiles}" $(basename ${bamFile})"
done
- for index in ~{sep=" " bamIndex};
+ for index in ~{sep=" " bamIndex}
do
ln ${index} .
done
@@ -110,13 +110,13 @@ task Bam2Fastq {
# Localise the bam and pbi files so they are next to each other in the
# current folder.
bamFiles=""
- for bamFile in ~{sep=" " bam};
+ for bamFile in ~{sep=" " bam}
do
ln ${bamFile} .
bamFiles=${bamFiles}" $(basename ${bamFile})"
done
- for index in ~{sep=" " bamIndex};
+ for index in ~{sep=" " bamIndex}
do
ln ${index} .
done
diff --git a/delly.wdl b/delly.wdl
index f708f4949fa74743e3655ab8d8c0e292ac0050c9..ffe9023a6221c24f0cfd0ba5b880d345269bc32a 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2018 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -59,9 +57,9 @@ task CallSV {
bamFile: {description: "The bam file to process.", category: "required"}
bamIndex: {description: "The index bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
- referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
+ referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
- memory: {description: "The memory required to run the programs", category: "advanced"}
+ memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 04b6813f3369c02debab54464e2627fea3a3ba42..dd3dfc2ea1cce232b0912afd75ac927336ea12a6 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -29,6 +29,7 @@ task Fastqc {
Boolean noFilter = false
Boolean extract = false
Boolean nogroup = false
+
Int? minLength
String? format
File? contaminants
@@ -37,32 +38,35 @@ task Fastqc {
Int? kmers
String? dir
- Int threads = 1
# Set javaXmx a little high. Equal to fastqc default with 7 threads.
# This is because some fastq files need more memory. 2G per core
# is a nice cluster default, so we use all the rest of the memory for
# fastqc so we should have as little OOM crashes as possible even with
# weird edge case fastq's.
- String javaXmx="1750M"
+ String javaXmx="1750M"
+ Int threads = 1
String memory = "2G"
Int timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
- String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
- Array[File]? NoneArray
- File? NoneFile
+ String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0
+
+ Array[File]? noneArray
+ File? noneFile
}
# Chops of the .gz extension if present.
- # The Basename needs to be taken here. Otherwise paths might differ between similar jobs.
+ # The Basename needs to be taken here. Otherwise paths might differ
+ # between similar jobs.
String name = basename(sub(seqFile, "\.gz$",""))
- # This regex chops of the extension and replaces it with _fastqc for the reportdir.
+ # This regex chops of the extension and replaces it with _fastqc for
+ # the reportdir.
# Just as fastqc does it.
String reportDir = outdirPath + "/" + sub(name, "\.[^\.]*$", "_fastqc")
- # We reimplement the perl wrapper here. This has the advantage that it gives
- # us more control over the amount of memory used.
+ # We reimplement the perl wrapper here. This has the advantage that it
+ # gives us more control over the amount of memory used.
command <<<
set -e
- mkdir -p ~{outdirPath}
+ mkdir -p "~{outdirPath}"
FASTQC_DIR="/usr/local/opt/fastqc-0.11.9"
export CLASSPATH="$FASTQC_DIR:$FASTQC_DIR/sam-1.103.jar:$FASTQC_DIR/jbzip2-0.9.jar:$FASTQC_DIR/cisd-jhdf5.jar"
java -Djava.awt.headless=true -XX:ParallelGCThreads=1 \
@@ -86,23 +90,24 @@ task Fastqc {
>>>
output {
- File? rawReport = if extract then reportDir + "/fastqc_data.txt" else NoneFile
File htmlReport = reportDir + ".html"
File reportZip = reportDir + ".zip"
- File? summary = if extract then reportDir + "/summary.txt" else NoneFile
- Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else NoneArray
+ File? summary = if extract then reportDir + "/summary.txt" else noneFile
+ File? rawReport = if extract then reportDir + "/fastqc_data.txt" else noneFile
+ Array[File]? images = if extract then glob(reportDir + "/Images/*.png") else noneArray
}
runtime {
cpu: threads
memory: memory
- docker: dockerImage
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
seqFile: {description: "A fastq file.", category: "required"}
- outdirPath: {description: "The path to write the output to", catgory: "required"}
+ outdirPath: {description: "The path to write the output to.", catgory: "required"}
casava: {description: "Equivalent to fastqc's --casava flag.", category: "advanced"}
nano: {description: "Equivalent to fastqc's --nano flag.", category: "advanced"}
noFilter: {description: "Equivalent to fastqc's --nofilter flag.", category: "advanced"}
@@ -115,18 +120,16 @@ task Fastqc {
limits: {description: "Equivalent to fastqc's --limits option.", category: "advanced"}
kmers: {description: "Equivalent to fastqc's --kmers option.", category: "advanced"}
dir: {description: "Equivalent to fastqc's --dir option.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
threads: {description: "The number of cores to use.", category: "advanced"}
- javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
meta {
WDL_AID: {
- exclude: ["NoneFile", "NoneArray"]
+ exclude: ["noneFile", "noneArray"]
}
}
}
@@ -155,14 +158,14 @@ task GetConfiguration {
}
runtime {
- memory: "2G" # Needs more than 1 to pull the docker image
+ memory: "2G" # Needs more than 1 to pull the docker image.
time_minute: timeMinutes
docker: dockerImage
}
parameter_meta {
+ # inputs
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
diff --git a/fastqsplitter.wdl b/fastqsplitter.wdl
index c523cf8a7dd4e86e65cc768daa3c98f98854b39f..25a50954323974554925a8ca1305aba63a1e49ee 100644
--- a/fastqsplitter.wdl
+++ b/fastqsplitter.wdl
@@ -1,7 +1,5 @@
version 1.0
-# MIT License
-#
# Copyright (c) 2019 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -26,19 +24,24 @@ task Fastqsplitter {
input {
File inputFastq
Array[String]+ outputPaths
- String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
+
Int? compressionLevel
Int? threadsPerFile
- # fastqplitter utilizes one thread per input file and one or more threads per output file + one thread for the application.
- # Since a compression level of 1 is used, each output file uses approx 0.5 cores.
+
+ # fastqplitter utilizes one thread per input file and one or
+ # more threads per output file + one thread for the application.
+ # Since a compression level of 1 is used, each output file
+ # uses approx 0.5 cores.
Int cores = 1 + ceil(0.5 * length(outputPaths))
+ String dockerImage = "quay.io/biocontainers/fastqsplitter:1.1.0--py37h516909a_1"
}
# Busybox mkdir does not accept multiple paths.
command <<<
set -e
for FILE in ~{sep=' ' outputPaths}
- do mkdir -p "$(dirname $FILE)"
+ do
+ mkdir -p "$(dirname ${FILE})"
done
fastqsplitter \
~{"-c " + compressionLevel} \
@@ -51,15 +54,16 @@ task Fastqsplitter {
Array[File] chunks = outputPaths
}
- # Using very safe margins here. 10MB/300MB per outputfile is used for single-threaded/multi-threaded compression.
+ # Using very safe margins here. 10MB/300MB per outputfile is used for
+ # single-threaded/multi-threaded compression.
Float memoryPerFile = if select_first([threadsPerFile, 1]) > 1 then 0.40 else 0.02
Int fastqsplitterMemory = ceil(0.100 + memoryPerFile * length(outputPaths))
- # Make sure a minimum of 2 GB is present to pull the singularity image
+ # Make sure a minimum of 2 GB is present to pull the singularity image.
Int memory = if fastqsplitterMemory <= 2 then 2 else fastqsplitterMemory
runtime {
+ cpu: cores
memory: "~{memory}G"
docker: dockerImage
- cpu: cores
}
}
diff --git a/flash.wdl b/flash.wdl
index 6e704921590264bf1477088a8944db729f0eaedd..c4554c50ff95b1c4d09258906ba5bfd26bdf8b03 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -24,13 +24,14 @@ import "common.wdl" as common
task Flash {
input {
- String? preCommand
FastqPair inputFastq
String outdirPath
String outPrefix = "flash"
+ Boolean compress = true
+
+ String? preCommand
Int? minOverlap
Int? maxOverlap
- Boolean compress = true
Int threads = 2
String memory = "2G"
@@ -55,8 +56,8 @@ task Flash {
File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
FastqPair notCombined = object {
- R1: notCombined1,
- R2: notCombined2
+ R1: notCombined1,
+ R2: notCombined2
}
File hist = outdirPath + "/" + outPrefix + ".hist"
File histogram = outdirPath + "/" + outPrefix + ".histogram"
@@ -66,5 +67,4 @@ task Flash {
cpu: threads
memory: memory
}
-
-}
\ No newline at end of file
+}
diff --git a/gatk.wdl b/gatk.wdl
index 12416dda147265aff574110d075f34f2897fdae7..cc5d1de5771d6c52b5fe8e3e0a9d33ea12c97623 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -28,12 +28,13 @@ task AnnotateIntervals {
String annotatedIntervalsPath = "intervals.annotated.tsv"
File intervals
String intervalMergingRule = "OVERLAPPING_ONLY"
+ Int featureQueryLookahead = 1000000
+
File? mappabilityTrack
File? segmentalDuplicationTrack
- Int featureQueryLookahead = 1000000
- String memory = "3G"
String javaXmx = "2G"
+ String memory = "3G"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -57,9 +58,9 @@ task AnnotateIntervals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -71,17 +72,15 @@ task AnnotateIntervals {
intervalMergingRule: {description: "Equivalent to gatk AnnotateIntervals' `--interval-merging-rule` option.", category: "advanced"}
mappabilityTrack: {description: "Equivalent to gatk AnnotateIntervals' `--mappability-track` option.", category: "common"}
segmentalDuplicationTrack: {description: "Equivalent to gatk AnnotateIntervals' `--segmenta-duplicarion-track` option.", category: "common"}
- featureQueryLookahead: {description: "Equivalent to gatk AnnotateIntervals' `--feature-query-lookahead` option", category: "advanced"}
+ featureQueryLookahead: {description: "Equivalent to gatk AnnotateIntervals' `--feature-query-lookahead` 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"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
-# Apply Base Quality Score Recalibration (BQSR) model
+# Apply Base Quality Score Recalibration (BQSR) model.
task ApplyBQSR {
input {
File inputBam
@@ -93,9 +92,11 @@ task ApplyBQSR {
File referenceFastaDict
File referenceFastaFai
- Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 2048
- Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
+ Int memoryMb = javaXmxMb + 512
+ # This will likely be used with intervals, as such size based
+ # estimation can't be used.
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -124,33 +125,29 @@ task ApplyBQSR {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file which should be recalibrated.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
-# Generate Base Quality Score Recalibration (BQSR) model
+# Generate Base Quality Score Recalibration (BQSR) model.
task BaseRecalibrator {
input {
File inputBam
@@ -159,14 +156,15 @@ task BaseRecalibrator {
Array[File] sequenceGroupInterval = []
Array[File] knownIndelsSitesVCFs = []
Array[File] knownIndelsSitesVCFIndexes = []
- File? dbsnpVCF
- File? dbsnpVCFIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- Int memoryMb = javaXmxMb + 512
+ File? dbsnpVCF
+ File? dbsnpVCFIndex
+
Int javaXmxMb = 1024
+ Int memoryMb = javaXmxMb + 512
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -190,42 +188,39 @@ task BaseRecalibrator {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
knownIndelsSitesVCFs: {description: "VCF files with known indels.", category: "advanced"}
knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs.", category: "advanced"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- 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"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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 CalculateContamination {
input {
File tumorPileups
+
File? normalPileups
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13G"
Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -246,20 +241,19 @@ task CalculateContamination {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
tumorPileups: {description: "The pileup summary of a tumor/case sample.", category: "required"}
normalPileups: {description: "The pileup summary of the normal/control sample.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -268,8 +262,8 @@ task CallCopyRatioSegments {
String outputPrefix
File copyRatioSegments
- String memory = "3G"
String javaXmx = "2G"
+ String memory = "3G"
Int timeMinutes = 2
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -289,20 +283,19 @@ task CallCopyRatioSegments {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
outputPrefix: {description: "The prefix for the output files.", category: "required"}
copyRatioSegments: {description: "The copy ratios file generated by gatk ModelSegments.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -310,15 +303,16 @@ task CollectAllelicCounts {
input {
String allelicCountsPath = "allelic_counts.tsv"
File commonVariantSites
- File? commonVariantSitesIndex
File inputBam
File inputBamIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- String memory = "11G"
+ File? commonVariantSitesIndex
+
String javaXmx = "10G"
+ String memory = "11G"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -339,26 +333,25 @@ task CollectAllelicCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
allelicCountsPath: {description: "The path the output should be written to.", category: "advanced"}
commonVariantSites: {description: "Interval list or vcf of common variant sites (to retrieve the allelic counts for).", category: "required"}
- commonVariantSitesIndex: {description: "The index for commonVariantSites.", category: "common"}
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"}
+ commonVariantSitesIndex: {description: "The index for commonVariantSites.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -373,8 +366,8 @@ task CollectReadCounts {
File referenceFastaFai
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "8G"
String javaXmx = "7G"
+ String memory = "8G"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 5)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -397,12 +390,13 @@ task CollectReadCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
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"}
@@ -411,12 +405,10 @@ task CollectReadCounts {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
intervalMergingRule: {description: "Equivalent to gatk CollectReadCounts' `--interval-merging-rule` option.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -430,8 +422,8 @@ task CombineGVCFs {
File referenceFastaDict
File referenceFastaFai
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 1 + ceil(size(gvcfFiles, "G") * 8)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -453,28 +445,24 @@ task CombineGVCFs {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFiles: {description: "The GVCF files to be combined.", category: "required"}
gvcfFilesIndex: {description: "The indexes for the GVCF files.", caregory: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
outputPath: {description: "The location the combined GVCF should be written to.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -486,12 +474,12 @@ task CombineVariants {
String genotypeMergeOption = "UNIQUIFY"
String filteredRecordsMergeType = "KEEP_IF_ANY_UNFILTERED"
Array[String]+ identifiers
- Array[File]+ variantVcfs # follow "identifiers" array order
+ Array[File]+ variantVcfs # Follow "identifiers" array order.
Array[File]+ variantIndexes
String outputPath
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13G"
Int timeMinutes = 180
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
@@ -499,17 +487,17 @@ task CombineVariants {
command <<<
set -e
mkdir -p "$(dirname ~{outputPath})"
-
- # build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
- # Make sure commands are run in bash
+ # Build "-V:<ID> <file.vcf>" arguments according to IDs
+ # and VCFs to merge.
+ # Make sure commands are run in bash.
V_args=$(bash -c '
set -eu
ids=(~{sep=" " identifiers})
vars=(~{sep=" " variantVcfs})
for (( i = 0; i < ${#ids[@]}; ++i ))
- do
+ do
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
- done
+ done
')
java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 -jar /usr/GenomeAnalysisTK.jar \
-T CombineVariants \
@@ -526,12 +514,13 @@ task CombineVariants {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
@@ -540,14 +529,11 @@ task CombineVariants {
identifiers: {description: "The sample identifiers in the same order as variantVcfs.", category: "required"}
variantVcfs: {description: "The input VCF files in the same order as identifiers.", category: "required"}
variantIndexes: {description: "The indexes of the input VCF files.", category: "required"}
- outputPath: {description: "The location the output should be written to", category: "required"}
-
+ outputPath: {description: "The location the output should be written to.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -555,10 +541,11 @@ task CreateReadCountPanelOfNormals {
input {
String PONpath = "PON.hdf5"
Array[File]+ readCountsFiles
+
File? annotatedIntervals
- String memory = "8G"
String javaXmx = "7G"
+ String memory = "8G"
Int timeMinutes = 5
String dockerImage = "broadinstitute/gatk:4.1.8.0" # The biocontainer causes a spark related error for some reason...
}
@@ -578,34 +565,33 @@ task CreateReadCountPanelOfNormals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
PONpath: {description: "The location the PON should be written to.", category: "common"}
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"}
+ annotatedIntervals: {description: "An annotation set of intervals as generated by AnnotateIntervals. If provided, explicit GC correction will be performed.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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 DenoiseReadCounts {
input {
- File? PON
- File? annotatedIntervals
File readCounts
String outputPrefix
- String memory = "5G"
+ File? PON
+ File? annotatedIntervals
+
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -628,23 +614,21 @@ task DenoiseReadCounts {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
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"}
+ # inputs
readCounts: {description: "The read counts file as generated by CollectReadCounts.", category: "required"}
outputPrefix: {description: "The prefix for the output files.", category: "required"}
+ 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"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -656,14 +640,15 @@ task FilterMutectCalls {
File unfilteredVcf
File unfilteredVcfIndex
String outputVcf
+ Int uniqueAltReadCount = 4
+ File mutect2Stats
+
File? contaminationTable
File? mafTumorSegments
File? artifactPriors
- Int uniqueAltReadCount = 4
- File mutect2Stats
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -692,41 +677,39 @@ task FilterMutectCalls {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
unfilteredVcf: {description: "An unfiltered VCF file as produced by Mutect2.", category: "required"}
unfilteredVcfIndex: {description: "The index of the unfiltered VCF file.", category: "required"}
outputVcf: {description: "The location the filtered VCF file should be written.", category: "required"}
+ uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
+ mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", category: "advanced"}
contaminationTable: {description: "Equivalent to FilterMutectCalls' `--contamination-table` option.", category: "advanced"}
mafTumorSegments: {description: "Equivalent to FilterMutectCalls' `--tumor-segmentation` option.", category: "advanced"}
artifactPriors: {description: "Equivalent to FilterMutectCalls' `--ob-priors` option.", category: "advanced"}
- uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
- mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
-# Combine multiple recalibration tables from scattered BaseRecalibrator runs
+# Combine multiple recalibration tables from scattered BaseRecalibrator runs.
task GatherBqsrReports {
input {
Array[File] inputBQSRreports
String outputReportPath
- Int memoryMb = 256 + javaXmxMb
Int javaXmxMb = 256
+ Int memoryMb = 256 + javaXmxMb
Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -745,21 +728,19 @@ task GatherBqsrReports {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBQSRreports: {description: "The BQSR reports to be merged.", category: "required"}
outputReportPath: {description: "The location of the combined BQSR report.", category: "required"}
-
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -770,9 +751,11 @@ task GenomicsDBImport {
Array[File]+ intervals
String genomicsDBWorkspacePath = "genomics_db"
String genomicsDBTarFile = "genomics_db.tar.gz"
+
String? tmpDir
- String memory = "5G"
+
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -794,25 +777,23 @@ task GenomicsDBImport {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFiles: {description: "The gvcfFiles to be merged.", category: "required"}
gvcfFilesIndex: {description: "Indexes for the gvcfFiles.", category: "required"}
intervals: {description: "intervals over which to operate.", category: "required"}
- genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored", category: "advanced"}
- genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored", category: "advanced"}
- tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers",
- category: "advanced"}
+ genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored.", category: "advanced"}
+ genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored.", category: "advanced"}
+ tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -820,18 +801,19 @@ task GenotypeGVCFs {
input {
File gvcfFile
File gvcfFileIndex
- Array[File]? intervals
String outputPath
File referenceFasta
File referenceFastaDict
File referenceFastaFai
Array[String] annotationGroups = ["StandardAnnotation"]
+
+ Array[File]? intervals
File? dbsnpVCF
File? dbsnpVCFIndex
File? pedigree
- String memory = "7G"
String javaXmx = "6G"
+ String memory = "7G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -854,35 +836,31 @@ task GenotypeGVCFs {
output {
File outputVCF = outputPath
File outputVCFIndex = outputPath + ".tbi"
-
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
gvcfFile: {description: "The GVCF file to be genotyped.", category: "required"}
gvcfFileIndex: {description: "The index of the input GVCF file.", category: "required"}
- intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "optional"}
outputPath: {description: "The location to write the output VCF file to.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
- annotationGroups: {description: "Which annotation groups will be used for the annotation", category: "advanced"}
+ annotationGroups: {description: "Which annotation groups will be used for the annotation.", category: "advanced"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "optional"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- pedigree: {description: "Pedigree file for determining the population \"founders\"", category: "common"}
+ pedigree: {description: "Pedigree file for determining the population \"founders\".", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -896,8 +874,8 @@ task GetPileupSummaries {
File sitesForContaminationIndex
String outputPrefix
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13G"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -917,12 +895,13 @@ task GetPileupSummaries {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
sampleBam: {description: "A BAM file for which a pileup should be created.", category: "required"}
sampleBamIndex: {description: "The index of the input BAM file.", category: "required"}
variantsForContamination: {description: "A VCF file with common variants.", category: "required"}
@@ -930,13 +909,10 @@ task GetPileupSummaries {
sitesForContamination: {description: "A bed file describing regions to operate on.", category: "required"}
sitesForContaminationIndex: {description: "The index for the bed file.", category: "required"}
outputPrefix: {description: "The prefix for the ouput.", category: "required"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -945,26 +921,27 @@ task HaplotypeCaller {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
- Array[File]+? intervalList
- Array[File]+? excludeIntervalList
String outputPath
File referenceFasta
File referenceFastaIndex
File referenceFastaDict
+ Boolean gvcf = false
+ String emitRefConfidence = if gvcf then "GVCF" else "NONE"
+ Boolean dontUseSoftClippedBases = false
+
+ Array[File]+? intervalList
+ Array[File]+? excludeIntervalList
Float? contamination
File? dbsnpVCF
File? dbsnpVCFIndex
File? pedigree
Int? ploidy
String? outputMode
- Boolean gvcf = false
- String emitRefConfidence = if gvcf then "GVCF" else "NONE"
- Boolean dontUseSoftClippedBases = false
Float? standardMinConfidenceThresholdForCalling
- Int memoryMb = javaXmxMb + 512
- # Memory increases with time used. 4G should cover most use cases.
Int javaXmxMb = 4096
+ # Memory increases with time used. 4G should cover most use cases.
+ Int memoryMb = javaXmxMb + 512
Int timeMinutes = 400 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -995,50 +972,44 @@ task HaplotypeCaller {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
- intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
- excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
outputPath: {description: "The location to write the output to.", category: "required"}
- ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
- gvcf: {description: "Whether the output should be a gvcf", category: "common"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaIndex: {description: "The index for the reference fasta file.", category: "required"}
- contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
- outputMode: {description: "Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.",
- category: "advanced"}
- emitRefConfidence: {description: "Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'",
- category: "advanced"}
+ gvcf: {description: "Whether the output should be a gvcf.", category: "common"}
+ emitRefConfidence: {description: "Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'.", category: "advanced"}
dontUseSoftClippedBases: {description: "Do not use soft-clipped bases. Should be 'true' for RNA variant calling.", category: "common"}
- standardMinConfidenceThresholdForCalling: {description: "Confidence threshold used for calling variants.", category: "advanced"}
+ intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
+ excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
+ contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- pedigree: {description: "Pedigree file for determining the population \"founders\"", category: "common"}
+ pedigree: {description: "Pedigree file for determining the population \"founders\".", category: "common"}
+ ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
+ outputMode: {description: "Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.", category: "advanced"}
+ standardMinConfidenceThresholdForCalling: {description: "Confidence threshold used for calling variants.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
- category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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 LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
- String memory = "13G"
String javaXmx = "12G"
+ String memory = "13G"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1056,19 +1027,18 @@ task LearnReadOrientationModel {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
f1r2TarGz: {description: "A f1r2TarGz file outputed by mutect2.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1076,8 +1046,8 @@ task MergeStats {
input {
Array[File]+ stats
- String memory = "15G"
String javaXmx = "14G"
+ String memory = "15G"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1095,19 +1065,18 @@ task MergeStats {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
stats: {description: "Statistics files to be merged.", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1117,14 +1086,13 @@ task ModelSegments {
String outputPrefix
File denoisedCopyRatios
File allelicCounts
- File? normalAllelicCounts
- Int minimumTotalAlleleCountCase = if defined(normalAllelicCounts)
- then 0
- else 30
+ Int minimumTotalAlleleCountCase = if defined(normalAllelicCounts) then 0 else 30
Int maximumNumberOfSmoothingIterations = 10
- String memory = "11G"
+ File? normalAllelicCounts
+
String javaXmx = "10G"
+ String memory = "11G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1145,7 +1113,6 @@ task ModelSegments {
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"
@@ -1155,29 +1122,28 @@ task ModelSegments {
File modeledSegments = outputDir + "/" + outputPrefix + ".modelFinal.seg"
File copyRatioParameters = outputDir + "/" + outputPrefix + ".modelFinal.cr.param"
File alleleFractionParameters = outputDir + "/" + outputPrefix + ".modelFinal.af.param"
+ File? normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
}
runtime {
- docker: dockerImage
- time_minute: timeMinutes
memory: memory
+ time_minute: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
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"}
-
+ normalAllelicCounts: {description: "The allelicCounts as generate by CollectAllelicCounts for a matched normal.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1190,17 +1156,18 @@ task MuTect2 {
File referenceFastaFai
String outputVcf
String tumorSample
+ String f1r2TarGz = "f1r2.tar.gz"
+ Array[File]+ intervals
+ String outputStats = outputVcf + ".stats"
+
String? normalSample
File? germlineResource
File? germlineResourceIndex
File? panelOfNormals
File? panelOfNormalsIndex
- String f1r2TarGz = "f1r2.tar.gz"
- Array[File]+ intervals
- String outputStats = outputVcf + ".stats"
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 240
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1229,12 +1196,13 @@ task MuTect2 {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
@@ -1242,20 +1210,18 @@ task MuTect2 {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
tumorSample: {description: "The name of the tumor/case sample.", category: "required"}
+ f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
+ intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
+ outputStats: {description: "The location the output statistics should be written to.", category: "advanced"}
normalSample: {description: "The name of the normal/control sample.", category: "common"}
germlineResource: {description: "Equivalent to Mutect2's `--germline-resource` option.", category: "advanced"}
germlineResourceIndex: {description: "The index for the germline resource.", category: "advanced"}
panelOfNormals: {description: "Equivalent to Mutect2's `--panel-of-normals` option.", category: "advanced"}
panelOfNormalsIndex: {description: "The index for the panel of normals.", category: "advanced"}
- f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
- intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
- outputStats: {description: "The location the output statistics should be written to.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1266,10 +1232,11 @@ task PlotDenoisedCopyRatios {
String outputPrefix
File standardizedCopyRatios
File denoisedCopyRatios
+
Int? minimumContigLength
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4G"
Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
@@ -1289,32 +1256,31 @@ task PlotDenoisedCopyRatios {
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"
+ File? denoisedCopyRatiosLimitedPlot = outputDir + "/" + outputPrefix + ".denoisedLimit4.png"
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
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"}
+ denoisedCopyRatios: {description: "The denoised copy ratios as generated by DenoiseReadCounts.", category: "required"}
minimumContigLength: {description: "The minimum length for a contig to be included in the plots.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1326,10 +1292,11 @@ task PlotModeledSegments {
File denoisedCopyRatios
File segments
File allelicCounts
+
Int? minimumContigLength
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4G"
Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
@@ -1353,12 +1320,13 @@ task PlotModeledSegments {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
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"}
@@ -1366,12 +1334,10 @@ task PlotModeledSegments {
segments: {description: "The modeled segments as generated by ModelSegments.", category: "required"}
allelicCounts: {description: "The hetrozygous allelic counts as generated by ModelSegments.", category: "required"}
minimumContigLength: {description: "The minimum length for a contig to be included in the plots.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1380,14 +1346,15 @@ task PreprocessIntervals {
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- File? intervals
String outputIntervalList = "bins.interval_list"
Int binLength = if defined(intervals) then 0 else 1000
Int padding = if defined(intervals) then 250 else 0
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "4G"
+ File? intervals
+
String javaXmx = "3G"
+ String memory = "4G"
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 6)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1411,41 +1378,42 @@ task PreprocessIntervals {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- referenceFasta: {description: "The reference fasta file..", category: "required"}
+ # inputs
+ 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"}
- intervals: {description: "Bed files describing the regiosn to operate on.", category: "common"}
outputIntervalList: {description: "The location the output should be written to.", category: "advanced"}
binLength: {description: "The size of the bins to be created. Should be 0 for targeted/exome sequencing.", category: "advanced"}
padding: {description: "The padding to be added to the bins. Should be 0 if contiguos binning is used, eg with WGS.", category: "advanced"}
intervalMergingRule: {description: "Equivalent to gatk PreprocessIntervals' `--interval-merging-rule` option.", category: "advanced"}
+ intervals: {description: "Bed files describing the regiosn to operate on.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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 SelectVariants {
input {
+ File inputVcf
+ File inputVcfIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- File inputVcf
- File inputVcfIndex
String outputPath = "output.vcf.gz"
- String? selectTypeToInclude
Array[File] intervals = []
- String memory = "5G"
+
+ String? selectTypeToInclude
+
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1468,29 +1436,25 @@ task SelectVariants {
}
runtime {
- docker: dockerImage
- time_minute: timeMinutes
memory: memory
+ time_minute: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputVcf: {description: "The VCF input file.", category: "required"}
inputVcfIndex: {description: "The input VCF file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
- selectTypeToInclude: {description: "Select only a certain type of variants from the input file", category: "common"}
outputPath: {description: "The location the output VCF file should be written.", category: "advanced"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
-
+ selectTypeToInclude: {description: "Select only a certain type of variants from the input file.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1504,8 +1468,8 @@ task SplitNCigarReads {
String outputBam
Array[File] intervals = []
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1527,28 +1491,24 @@ task SplitNCigarReads {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputBam: {description: "The BAM file for which spliced reads should be split.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
outputBam: {description: "The location the output BAM file should be written.", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
@@ -1558,11 +1518,6 @@ task VariantEval {
Array[File] evalVcfsIndex
Array[File] comparisonVcfs = []
Array[File] comparisonVcfsIndex = []
- File? referenceFasta
- File? referenceFastaDict
- File? referenceFastaFai
- File? dbsnpVCF
- File? dbsnpVCFIndex
Array[File] intervals = []
String outputPath = "eval.table"
Boolean doNotUseAllStandardModules = false
@@ -1572,8 +1527,14 @@ task VariantEval {
Array[String] samples = []
Boolean mergeEvals = false
- String memory = "5G"
+ File? referenceFasta
+ File? referenceFastaDict
+ File? referenceFastaFai
+ File? dbsnpVCF
+ File? dbsnpVCFIndex
+
String javaXmx = "4G"
+ String memory = "5G"
# TODO: Refine estimate. For now 4 minutes per GB of input.
Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs, select_all([referenceFasta, dbsnpVCF])]), "G") * 20)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
@@ -1604,35 +1565,37 @@ task VariantEval {
runtime {
cpu: 1
- docker: dockerImage
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
+
parameter_meta {
+ # inputs
evalVcfs: {description: "Variant sets to evaluate.", category: "required"}
evalVcfsIndex: {description: "Indexes for the variant sets.", category: "required"}
comparisonVcfs: {description: "Compare set vcfs.", category: "advanced"}
comparisonVcfsIndex: {description: "Indexes for the compare sets.", category: "advanced"}
- evalModules: {description: "One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless doNotUseAllStandardModules=true)", category: "common"}
- stratificationModules: {description: "One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless doNotUseAllStandardStratifications=true)", category: "common"}
- samples: {description: "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context." , category: "advanced"} # Advanced because this description is impossible to understand...
- mergeEvals: {description: "If provided, all evalVcf tracks will be merged into a single eval track", category: "common"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
+ outputPath: {description: "The location the output table should be written.", category: "advanced"}
doNotUseAllStandardModules: {description: "Do not use the standard modules by default (instead, only those that are specified with the evalModules option).", category: "common"}
doNotUseAllStandardStratifications: {description: "Do not use the standard stratification modules by default (instead, only those that are specified with the stratificationModules option).", category: "common"}
+ evalModules: {description: "One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless doNotUseAllStandardModules=true).", category: "common"}
+ stratificationModules: {description: "One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless doNotUseAllStandardStratifications=true).", category: "common"}
+ samples: {description: "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context." , category: "advanced"}
+ mergeEvals: {description: "If provided, all evalVcf tracks will be merged into a single eval track.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "common"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "common"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "common"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
- outputPath: {description: "The location the output table should be written.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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 VariantFiltration {
input {
File inputVcf
@@ -1644,8 +1607,8 @@ task VariantFiltration {
Array[String]+ filterArguments
Array[File] intervals = []
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
@@ -1668,29 +1631,24 @@ task VariantFiltration {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
+ # inputs
inputVcf: {description: "The VCF to be filtered.", category: "required"}
inputVcfIndex: {description: "The input VCF file's index.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", 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"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ filterArguments: {description: "Arguments that should be used for the filter. For example: ['--filter-name', 'my_filter', '--filter-expression', 'AB<0.2'].", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
- filterArguments: {description: "Arguments that should be used for the filter. For example: ['--filter-name', 'my_filter', '--filter-expression', 'AB<0.2']",
- category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+ 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"}
}
}
-
diff --git a/gffcompare.wdl b/gffcompare.wdl
index e5f62b5ec557ef05afbfcee0bb24d175a2b316b6..5d80f61994d4359555a16ee13e510c1d122ce0b0 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -147,4 +147,4 @@ task GffCompare {
exclude: ["noneFile"]
}
}
-}
\ No newline at end of file
+}