diff --git a/.travis.yml b/.travis.yml
index 7019e07a4fde725b05e6e8d355f3f9574e81d428..5109f9559d081a6b80af67c9993aff943af688ac 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,8 +1,26 @@
-language: java
+# We use conda to install cromwell.
+
+language: python
+
+python:
+ - 3.6
+
+before_install:
+ # Install conda
+ - export MINICONDA=${HOME}/miniconda
+ - export PATH=${MINICONDA}/bin:${PATH}
+ - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+ - bash miniconda.sh -b -f -p ${MINICONDA}
+ - conda config --set always_yes yes
+ - conda config --add channels defaults
+ - conda config --add channels bioconda
+ - conda config --add channels conda-forge
+
+install:
+ - conda install cromwell
+
script:
-- set -e
-- export CROMWELL_VERSION=35
-- wget https://github.com/broadinstitute/cromwell/releases/download/$CROMWELL_VERSION/womtool-$CROMWELL_VERSION.jar
-- for F in `find -name "*.wdl"`; do echo $F; java -jar womtool-*.jar validate $F; done
-- 'if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then git submodule foreach --recursive git checkout $TRAVIS_BRANCH && git submodule foreach --recursive git pull; fi'
-- "git diff --exit-code || (echo ERROR: Git changes detected. Please update submodules && exit 1)"
+ - set -e
+ - for FILE in $(find -name "*.wdl"); do echo $FILE; womtool validate $FILE; done
+ - 'if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then git submodule foreach git checkout develop && git submodule foreach git pull; fi'
+ - "git diff --exit-code || (echo ERROR: Git changes detected. Please update submodules && exit 1)"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bcdcc6f41972cc47859927af8753ce90b508e931..ce2247333cc077426083ac9cb04f707603be2bcb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,24 @@ that users understand how the changes affect the new version.
version 1.0.0-dev
---------------------------
++ Removed "pipefail" from command sections TALON and TranscriptClean
++ Add WDL task for Minimap2
++ Add WDL task for TALON
++ Add WDL task for TranscriptClean
++ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir
++ Cutadapt: simplify interface
++ Bigger memory multiplier in mutect to take in account bigger vmem usage
++ Cutadapt: Remove default adapter
++ Fastqsplitter: use version 1.1.
++ Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency
++ Common: Update dockerTag to dockerImage.
++ GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers.
++ Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
++ Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0.
++ Mutect2: Add necessary missing index attribute for panel of normals.
++ MultiQC: Add memory variable to multiqc task.
++ GATK: SplitNCigarReads, BaseRecalibration and ApplyBQSR do no longer need regions files as required inputs.
++ VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
+ Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
+ Cutadapt: Fix issues with read2output when using single-end reads.
+ Add feature type, idattr and additional attributes to htseq-count.
diff --git a/common.wdl b/common.wdl
index 7b85d461c58869e45cc818344ffb4d24e2f293d2..5c53c7727e3ecf5e11a66761dbf1693f13d8156e 100644
--- a/common.wdl
+++ b/common.wdl
@@ -77,7 +77,7 @@ task Copy {
Boolean recursive = false
# Version not that important as long as it is stable.
- String dockerTag = "5.0.2"
+ String dockerImage = "bash:5.0.2"
}
command {
@@ -91,7 +91,7 @@ task Copy {
}
runtime {
- docker: "bash:" + dockerTag
+ docker: dockerImage
}
}
@@ -155,7 +155,7 @@ task YamlToJson {
input {
File yaml
String outputJson = basename(yaml, "\.ya?ml$") + ".json"
- String dockerTag = "3.13-py37-slim"
+ String dockerImage = "biowdl/pyyaml:3.13-py37-slim"
}
command {
set -e
@@ -174,7 +174,7 @@ task YamlToJson {
}
runtime {
- docker: "biowdl/pyyaml:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 84ba9b59db9a0db17f70e1aa6fe72564380c0909..f3e8e29e167df6fba7156cd2f65d71f4adfc0c8b 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -7,16 +7,12 @@ task Cutadapt {
String read1output = "cut_r1.fq.gz"
String? read2output
String? format
- Array[String]+? adapter
- Array[String]+? front
- Array[String]+? anywhere
- Array[String]+? adapterRead2
- Array[String]+? frontRead2
- Array[String]+? anywhereRead2
- # FIXME: default should be set at the subworkflow level, not here. Needs to wait for cromwell fix.
- Array[String]+? adapterBoth = ["AGATCGGAAGAG"]
- # contaminations = anywhereBoth
- Array[String]+? contaminations
+ Array[String] adapter = []
+ Array[String] front = []
+ Array[String] anywhere = []
+ Array[String] adapterRead2 = []
+ Array[String] frontRead2 = []
+ Array[String] anywhereRead2 = []
Boolean? interleaved
String? pairFilter
Float? errorRate
@@ -74,25 +70,7 @@ task Cutadapt {
then "mkdir -p $(dirname " + realRead2output + ")"
else ""
- # FIXME: This crappy overengineering can be removed once cromwell can handle subworkflow inputs correctly.
- # Some WDL magic here to set both adapters with one setting.
- # If then else's are needed to keep the variable optional and undefined
- Array[String]+? adapterForward = if (defined(adapter) || defined(adapterBoth))
- then select_first([adapter, adapterBoth])
- else adapter
- # Check if read2 is defined before applying adapters.
- Array[String]+? adapterReverse = if (defined(read2) && (defined(adapterRead2) || defined(adapterBoth)))
- then select_first([adapterRead2, adapterBoth])
- else adapterRead2
-
- # Same for contaminations
- Array[String]+? anywhereForward = if (defined(anywhere) || defined(contaminations))
- then select_first([anywhere, contaminations])
- else anywhere
- Array[String]+? anywhereReverse = if (defined(read2) && (defined(anywhereRead2) || defined(contaminations)))
- then select_first([anywhereRead2, contaminations])
- else anywhereRead2
-
+ # FIXME: Use prefix() function for adapter, adapterRead2, etc.
command {
set -e
~{"mkdir -p $(dirname " + read1output + ")"}
@@ -100,12 +78,12 @@ task Cutadapt {
cutadapt \
~{"--cores=" + cores} \
~{true="-Z" false="" Z} \
- ~{true="-a" false="" defined(adapterForward)} ~{sep=" -a " adapterForward} \
- ~{true="-A" false="" defined(adapterReverse)} ~{sep=" -A " adapterReverse} \
- ~{true="-g" false="" defined(front)} ~{sep=" -g " front} \
- ~{true="-G" false="" defined(frontRead2)} ~{sep=" -G " frontRead2} \
- ~{true="-b" false="" defined(anywhereForward)} ~{sep=" -b " anywhereForward} \
- ~{true="-B" false="" defined(anywhereReverse)} ~{sep=" -B " anywhereReverse} \
+ ~{true="-a" false="" length(adapter) > 0} ~{sep=" -a " adapter} \
+ ~{true="-A" false="" length(adapterRead2) > 0} ~{sep=" -A " adapterRead2} \
+ ~{true="-g" false="" length(front) > 0} ~{sep=" -g " front} \
+ ~{true="-G" false="" length(frontRead2) > 0} ~{sep=" -G " frontRead2} \
+ ~{true="-b" false="" length(anywhere) > 0} ~{sep=" -b " anywhere} \
+ ~{true="-B" false="" length(anywhereRead2) > 0} ~{sep=" -B " anywhereRead2} \
--output ~{read1output} ~{if defined(read2) then "-p " + realRead2output else ""} \
~{"--to-short-output " + tooShortOutputPath} \
~{"--to-short-paired-output " + tooShortPairedOutputPath} \
diff --git a/fastqsplitter.wdl b/fastqsplitter.wdl
index 66f79af605d4f3bd9f28c3fa7690bb9808a5147c..cbbb7f307595c0e4732f82e8ee9f983cb81f944f 100644
--- a/fastqsplitter.wdl
+++ b/fastqsplitter.wdl
@@ -26,7 +26,7 @@ task Fastqsplitter {
input {
File inputFastq
Array[String]+ outputPaths
- String dockerImage = "quay.io/biocontainers/fastqsplitter:1.0.0--py_0"
+ 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.
@@ -34,15 +34,18 @@ task Fastqsplitter {
Int cores = 1 + ceil(0.5 * length(outputPaths))
}
- command {
+ # Busybox mkdir does not accept multiple paths.
+ command <<<
set -e
- mkdir -p $(dirname ~{sep=' ' outputPaths})
+ for FILE in ~{sep=' ' outputPaths}
+ do mkdir -p $(dirname $FILE)
+ done
fastqsplitter \
~{"-c " + compressionLevel} \
~{"-t " + threadsPerFile} \
-i ~{inputFastq} \
-o ~{sep=' -o ' outputPaths}
- }
+ >>>
output {
Array[File] chunks = outputPaths
diff --git a/gatk.wdl b/gatk.wdl
index 87fa1046be22020b0a7b37b638d6c30084c43519..9504de2d6bed80c7aa57618ce53242489b46018d 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -7,7 +7,7 @@ task ApplyBQSR {
File inputBamIndex
String outputBamPath
File recalibrationReport
- Array[File]+ sequenceGroupInterval
+ Array[File] sequenceGroupInterval = []
File referenceFasta
File referenceFastaDict
File referenceFastaFai
@@ -32,7 +32,7 @@ task ApplyBQSR {
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
- -L ~{sep=" -L " sequenceGroupInterval}
+ ~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
}
output {
@@ -53,7 +53,7 @@ task BaseRecalibrator {
File inputBam
File inputBamIndex
String recalibrationReportPath
- Array[File]+ sequenceGroupInterval
+ Array[File] sequenceGroupInterval = []
Array[File]? knownIndelsSitesVCFs
Array[File]? knownIndelsSitesVCFIndexes
File? dbsnpVCF
@@ -82,7 +82,7 @@ task BaseRecalibrator {
--use-original-qualities \
-O ~{recalibrationReportPath} \
--known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
- -L ~{sep=" -L " sequenceGroupInterval}
+ ~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
}
output {
@@ -258,12 +258,17 @@ task MuTect2 {
String outputVcf
String tumorSample
String? normalSample
+ File? germlineResource
+ File? germlineResourceIndex
File? panelOfNormals
+ File? panelOfNormalsIndex
+ String f1r2TarGz = "f1r2.tar.gz"
Array[File]+ intervals
+ String outputStats = outputVcf + ".stats"
Int memory = 4
- Float memoryMultiplier = 3
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ Float memoryMultiplier = 4
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
@@ -275,7 +280,9 @@ task MuTect2 {
-I ~{sep=" -I " inputBams} \
-tumor ~{tumorSample} \
~{"-normal " + normalSample} \
+ ~{"--germline-resource " + germlineResource} \
~{"--panel-of-normals " + panelOfNormals} \
+ ~{"--f1r2-tar-gz " + f1r2TarGz} \
-O ~{outputVcf} \
-L ~{sep=" -L " intervals}
}
@@ -283,6 +290,178 @@ task MuTect2 {
output {
File vcfFile = outputVcf
File vcfFileIndex = outputVcf + ".tbi"
+ File f1r2File = f1r2TarGz
+ File stats = outputStats
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task LearnReadOrientationModel {
+ input {
+ Array[File]+ f1r2TarGz
+
+ Int memory = 12
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ LearnReadOrientationModel \
+ -I ~{sep=" -I " f1r2TarGz} \
+ -O "artifact-priors.tar.gz"
+ }
+
+ output {
+ File artifactPriorsTable = "artifact-priors.tar.gz"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task MergeStats {
+ input {
+ Array[File]+ stats
+
+ Int memory = 14
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ MergeMutectStats \
+ -stats ~{sep=" -stats " stats} \
+ -O "merged.stats"
+ }
+
+ output {
+ File mergedStats = "merged.stats"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task GetPileupSummaries {
+ input {
+ File sampleBam
+ File sampleBamIndex
+ File variantsForContamination
+ File variantsForContaminationIndex
+ File sitesForContamination
+ File sitesForContaminationIndex
+ String outputPrefix
+
+ Int memory = 12
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ GetPileupSummaries \
+ -I ~{sampleBam} \
+ -V ~{variantsForContamination} \
+ -L ~{sitesForContamination} \
+ -O ~{outputPrefix + "-pileups.table"}
+ }
+
+ output {
+ File pileups = outputPrefix + "-pileups.table"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task CalculateContamination {
+ input {
+ File tumorPileups
+ File? normalPileups
+
+ Int memory = 12
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ CalculateContamination \
+ -I ~{tumorPileups} \
+ ~{"-matched " + normalPileups} \
+ -O "contamination.table" \
+ --tumor-segmentation "segments.table"
+ }
+
+ output {
+ File contaminationTable = "contamination.table"
+ File mafTumorSegments = "segments.table"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task FilterMutectCalls {
+ input {
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ File unfilteredVcf
+ File unfilteredVcfIndex
+ String outputVcf
+ File? contaminationTable
+ File? mafTumorSegments
+ File? artifactPriors
+ Int uniqueAltReadCount = 4
+ File mutect2Stats
+ String? extraArgs
+
+ Int memory = 12
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputVcf})
+ gatk --java-options -Xmx~{memory}G \
+ FilterMutectCalls \
+ -R ~{referenceFasta} \
+ -V ~{unfilteredVcf} \
+ -O ~{outputVcf} \
+ ~{"--contamination-table " + contaminationTable} \
+ ~{"--tumor-segmentation " + mafTumorSegments} \
+ ~{"--ob-priors " + artifactPriors} \
+ ~{"--unique-alt-read-count " + uniqueAltReadCount} \
+ ~{"-stats " + mutect2Stats} \
+ --filtering-stats "filtering.stats" \
+ --showHidden \
+ ~{extraArgs}
+ }
+
+ output {
+ File filteredVcf = outputVcf
+ File filteredVcfIndex = outputVcf + ".tbi"
+ File filteringStats = "filtering.stats"
}
runtime {
@@ -299,7 +478,7 @@ task SplitNCigarReads {
File referenceFastaDict
File referenceFastaFai
String outputBam
- Array[File]+ intervals
+ Array[File] intervals = []
Int memory = 4
Float memoryMultiplier = 4
@@ -314,7 +493,7 @@ task SplitNCigarReads {
-I ~{inputBam} \
-R ~{referenceFasta} \
-O ~{outputBam} \
- -L ~{sep=' -L ' intervals}
+ ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
}
output {
@@ -327,3 +506,59 @@ task SplitNCigarReads {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task CombineVariants {
+ input {
+ String installDir = "/usr" # .jar location in the docker image
+
+ File referenceFasta
+ File referenceFastaFai
+ File referenceFastaDict
+ String genotypeMergeOption = "UNIQUIFY"
+ String filteredRecordsMergeType = "KEEP_IF_ANY_UNFILTERED"
+ Array[String]+ identifiers
+ Array[File]+ variantVcfs # follow "identifiers" array order
+ Array[File]+ variantIndexes
+ String outputPath
+
+ Int memory = 12
+ Float memoryMultiplier = 2
+ String dockerImage = "broadinstitute/gatk3:3.8-1"
+ }
+
+ command <<<
+ set -e
+ mkdir -p $(dirname "~{outputPath}")
+
+ # build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
+ # Make sure commands are run in bash
+ bash -c '#!/usr/bin/env bash
+ set -eux
+ ids=(~{sep=" " identifiers})
+ vars=(~{sep=" " variantVcfs})
+ V_args=$(
+ for (( i = 0; i < ${#ids[@]}; ++i ))
+ do
+ printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
+ done
+ )
+ java -Xmx~{memory}G -jar ~{installDir}/GenomeAnalysisTK.jar \
+ -T CombineVariants \
+ -R ~{referenceFasta} \
+ --genotypemergeoption ~{genotypeMergeOption} \
+ --filteredrecordsmergetype ~{filteredRecordsMergeType} \
+ --out ~{outputPath} \
+ $V_args
+ '
+ >>>
+
+ output {
+ File combinedVcf = outputPath
+ File combinedVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
diff --git a/minimap2.wdl b/minimap2.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..b4e4d4ee63438570e0512c514565b41f647754fc
--- /dev/null
+++ b/minimap2.wdl
@@ -0,0 +1,142 @@
+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Indexing {
+ input {
+ File referenceFile
+ String outputPrefix
+ Boolean useHomopolymerCompressedKmer = false
+ Int kmerSize = 15
+ Int minimizerWindowSize = 10
+
+ Int? splitIndex
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ minimap2 \
+ ~{true="-H" false="" useHomopolymerCompressedKmer} \
+ ~{"-k " + kmerSize} \
+ ~{"-w " + minimizerWindowSize} \
+ ~{"-I " + splitIndex} \
+ ~{"-d " + outputPrefix + ".mmi"} \
+ ~{"-t " + cores} \
+ ~{referenceFile}
+ }
+
+ output {
+ File outputIndexFile = outputPrefix + ".mmi"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ referenceFile: "Reference fasta file."
+ outputPrefix: "Output directory path + output file prefix."
+ useHomopolymerCompressedKmer: "Use homopolymer-compressed k-mer (preferrable for PacBio)."
+ kmerSize: "K-mer size (no larger than 28)."
+ minimizerWindowSize: "Minimizer window size."
+ splitIndex: "Split index for every ~NUM input bases."
+
+ outputIndexFile: "Indexed reference file."
+ }
+}
+
+task Mapping {
+ input {
+ File queryFile
+ File referenceFile
+ String outputPrefix
+ String presetOption
+ Boolean outputSAM = false
+
+ Int? maxFragmentLength
+ Int? maxIntronLength
+ Boolean? skipSelfAndDualMappings
+ Int? retainMaxSecondaryAlignments
+ Int? matchingScore
+ Int? mismatchPenalty
+ String? howToFindGTAG
+ Boolean? secondaryAlignment
+
+ Int cores = 4
+ Int memory = 7
+ String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ minimap2 \
+ ~{"-x " + presetOption} \
+ ~{true="-a" false="" outputSAM} \
+ ~{"-G " + maxIntronLength} \
+ ~{"-F " + maxFragmentLength} \
+ ~{true="-X" false="" skipSelfAndDualMappings} \
+ ~{"-N " + retainMaxSecondaryAlignments} \
+ ~{"-A " + matchingScore} \
+ ~{"-B " + mismatchPenalty} \
+ ~{"-u " + howToFindGTAG} \
+ --secondary=~{true="yes" false="no" secondaryAlignment} \
+ ~{"-o " + outputPrefix} \
+ ~{"-t " + cores} \
+ ~{referenceFile} \
+ ~{queryFile}
+ }
+
+ output {
+ File outputAlignmentFile = outputPrefix
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ queryFile: "Input fasta file."
+ referenceFile: "Reference fasta file."
+ outputPrefix: "Output directory path + output file prefix."
+ presetOption: "This option applies multiple options at the same time."
+ outputSAM: "Output in the SAM format."
+ maxFragmentLength: "Max fragment length (effective with -xsr or in the fragment mode)."
+ maxIntronLength: "Max intron length (effective with -xsplice; changing -r)."
+ skipSelfAndDualMappings: "Skip self and dual mappings (for the all-vs-all mode)."
+ retainMaxSecondaryAlignments: "Retain at most INT secondary alignments."
+ matchingScore: "Matching score."
+ mismatchPenalty: "Mismatch penalty."
+ howToFindGTAG: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG."
+ secondaryAlignment: "Whether to output secondary alignments."
+
+ outputAlignmentFile: "Mapping and alignment between collections of DNA sequences file."
+ }
+}
diff --git a/multiqc.wdl b/multiqc.wdl
index e7a87e1490931ea84ccf156aa4c54f349d668292..fc5d49a70609702910a3958dad729c4ca983ad99 100644
--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -38,6 +38,7 @@ task MultiQC {
Boolean verbose = false
Boolean quiet = false
Array[Boolean] finished = [] # An array of booleans that can be used to let multiqc wait on stuff.
+ Int memory = 4
}
command {
@@ -86,6 +87,7 @@ task MultiQC {
}
runtime {
+ memory: memory
docker: dockerImage
}
}
diff --git a/picard.wdl b/picard.wdl
index 0dcb7ecd15ad8706b985b6c473e2dc180f53a644..450b475e60bd6191f0c9013392774e2f3ab096d8 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -8,7 +8,7 @@ task BedToIntervalList {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -52,9 +52,7 @@ task CollectMultipleMetrics {
Int memory = 8
Float memoryMultiplier = 4
- # https://raw.githubusercontent.com/BioContainers/multi-package-containers/80886dfea00f3cd9e7ae2edf4fc42816a10e5403/combinations/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923%3A8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0.tsv
- # Contains r-base=3.4.1,picard=2.18.2
- String dockerImage = "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -137,9 +135,7 @@ task CollectRnaSeqMetrics {
Int memory = 8
Float memoryMultiplier = 4.0
- # https://raw.githubusercontent.com/BioContainers/multi-package-containers/80886dfea00f3cd9e7ae2edf4fc42816a10e5403/combinations/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923%3A8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0.tsv
- # Contains r-base=3.4.1,picard=2.18.2
- String dockerImage = "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -178,7 +174,7 @@ task CollectTargetedPcrMetrics {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -216,7 +212,7 @@ task GatherBamFiles {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -250,7 +246,7 @@ task GatherVcfs {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -282,7 +278,7 @@ task MarkDuplicates {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
# Sometimes we wish to supply "null" in order to turn off optical duplicate detection
@@ -335,7 +331,7 @@ task MergeVCFs {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
# Using MergeVcfs instead of GatherVcfs so we can create indices
@@ -369,7 +365,7 @@ task SamToFastq {
Int memory = 16 # High memory default to avoid crashes.
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
File? NONE
}
@@ -406,7 +402,7 @@ task ScatterIntervalList {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
@@ -441,7 +437,7 @@ task SortVcf {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index d1163b4a1fcda41b45f9e3a12e7eb5b2ad16c882..7a25a0817950525000d53e2b13eccf4d79bfa323 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -267,3 +267,35 @@ task ParallelSingleTrain {
docker: dockerImage
}
}
+
+task ModifyStrelka {
+ input {
+ String installDir = "/opt/somaticseq/vcfModifier" #the location in the docker image
+
+ File strelkaVCF
+ String? outputVCFName = basename(strelkaVCF, ".gz")
+
+ Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
+ }
+
+ command {
+ set -e
+
+ ~{installDir}/modify_Strelka.py \
+ -infile ~{strelkaVCF} \
+ -outfile "modified_strelka.vcf"
+
+ first_FORMAT_line_num=$(grep -n -m 1 '##FORMAT' "modified_strelka.vcf" | cut -d : -f 1)
+ sed "$first_FORMAT_line_num"'i##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' "modified_strelka.vcf" > ~{outputVCFName}
+ }
+
+ output {
+ File outputVcf = outputVCFName
+ }
+
+ runtime {
+ cpu: threads
+ docker: dockerImage
+ }
+}
diff --git a/talon.wdl b/talon.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..507e0b9a3440a85a6109d81d2fb94d0c648e6343
--- /dev/null
+++ b/talon.wdl
@@ -0,0 +1,362 @@
+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task CreateAbundanceFileFromDatabase {
+ input {
+ File databaseFile
+ String outputPrefix
+ String genomeBuild
+ String annotationVersion
+ Boolean filterTranscripts = false
+
+ File? filterPairingsFile
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ create_abundance_file_from_database \
+ ~{"--db=" + databaseFile} \
+ ~{"--o=" + outputPrefix} \
+ ~{"-b " + genomeBuild} \
+ ~{"-a " + annotationVersion} \
+ ~{true="--filter" false="" filterTranscripts} \
+ ~{"-p " + filterPairingsFile}
+ }
+
+ output {
+ File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ databaseFile: "TALON database."
+ outputPrefix: "Output directory path + output file prefix."
+ genomeBuild: "Genome build to use."
+ annotationVersion: "Which annotation version to use."
+ filterTranscripts: "The transcripts in the database will be filtered prior to GTF creation."
+ filterPairingsFile: "A file indicating which datasets should be considered together."
+
+ outputAbundanceFile: "Abundance for each transcript in the TALON database across datasets."
+ }
+}
+
+task CreateGtfAbundanceFromDatabase {
+ input {
+ File databaseFile
+ String outputPrefix
+ String genomeBuild
+ String annotationVersion
+ Boolean filterTranscripts = false
+
+ File? filterPairingsFile
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ create_GTF_abundance_from_database \
+ ~{"--db=" + databaseFile} \
+ ~{"--o=" + outputPrefix} \
+ ~{"-b " + genomeBuild} \
+ ~{"-a " + annotationVersion} \
+ ~{true="--filter" false="" filterTranscripts} \
+ ~{"-p " + filterPairingsFile}
+ }
+
+ output {
+ File outputGTFfile = outputPrefix + "_talon_observedOnly.gtf"
+ File outputAbundanceFile = outputPrefix + "_talon_abundance.tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ databaseFile: "TALON database."
+ outputPrefix: "Output directory path + output file prefix."
+ genomeBuild: "Genome build to use."
+ annotationVersion: "Which annotation version to use."
+ filterTranscripts: "The transcripts in the database will be filtered prior to GTF creation."
+ filterPairingsFile: "A file indicating which datasets should be considered together."
+
+ outputGTFfile: "The genes, transcripts, and exons stored a TALON database in GTF format."
+ outputAbundanceFile: "Abundance for each transcript in the TALON database across datasets."
+ }
+}
+
+task CreateGtfFromDatabase {
+ input {
+ File databaseFile
+ String outputPrefix
+ String genomeBuild
+ String annotationVersion
+ Boolean observedInDataset = false
+
+ File? whitelistFile
+ File? datasetFile
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ create_GTF_from_database \
+ ~{"--db=" + databaseFile} \
+ ~{"--o=" + outputPrefix} \
+ ~{"-b " + genomeBuild} \
+ ~{"-a " + annotationVersion} \
+ ~{"--whitelist=" + whitelistFile} \
+ ~{true="--observed" false="" observedInDataset} \
+ ~{"-d " + datasetFile}
+ }
+
+ output {
+ File outputGTFfile = outputPrefix + "_talon.gtf"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ databaseFile: "TALON database."
+ outputPrefix: "Output directory path + output file prefix."
+ genomeBuild: "Genome build to use."
+ annotationVersion: "Which annotation version to use."
+ observedInDataset: "Output only includes transcripts that were observed at least once."
+ whitelistFile: "Whitelist file of transcripts to include in the output."
+ datasetFile: "A file indicating which datasets should be included."
+
+ outputGTFfile: "The genes, transcripts, and exons stored a TALON database in GTF format."
+ }
+}
+
+task InitializeTalonDatabase {
+ input {
+ File GTFfile
+ String outputPrefix
+ String genomeBuild
+ String annotationVersion
+ Int minimumLength = 300
+ String novelIDprefix = "TALON"
+ Int cutoff5p = 500
+ Int cutoff3p = 300
+
+ Int cores = 1
+ Int memory = 10
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ initialize_talon_database \
+ ~{"--f=" + GTFfile} \
+ ~{"--o=" + outputPrefix} \
+ ~{"--g=" + genomeBuild} \
+ ~{"--a=" + annotationVersion} \
+ ~{"--l=" + minimumLength} \
+ ~{"--idprefix=" + novelIDprefix} \
+ ~{"--5p=" + cutoff5p} \
+ ~{"--3p=" + cutoff3p}
+ }
+
+ output {
+ File outputDatabase = outputPrefix + ".db"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ GTFfile: "GTF annotation containing genes, transcripts, and edges."
+ outputPrefix: "Output directory path + output file prefix."
+ genomeBuild: "Name of genome build that the GTF file is based on (ie hg38)."
+ annotationVersion: "Name of supplied annotation (will be used to label data)."
+ minimumLength: "Minimum required transcript length."
+ novelIDprefix: "Prefix for naming novel discoveries in eventual TALON runs."
+ cutoff5p: "Maximum allowable distance (bp) at the 5' end during annotation."
+ cutoff3p: "Maximum allowable distance (bp) at the 3' end during annotation."
+
+ outputDatabase: "TALON database."
+ }
+}
+
+task MapAntisenseGenesToSense {
+ input {
+ File databaseFile
+ String outputPrefix
+ String annotationVersion
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ map_antisense_genes_to_sense \
+ ~{"--db=" + databaseFile} \
+ ~{"--o=" + outputPrefix} \
+ ~{"-a " + annotationVersion}
+ }
+
+ output {
+ File outputAntisenseMapFile = outputPrefix + "_antisense_mapping.gtf"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ databaseFile: "TALON database."
+ outputPrefix: "Output directory path + output file prefix."
+ annotationVersion: "Which annotation version to use."
+
+ outputAntisenseMapFile: "IDs of the sense gene for every antisense gene in the database."
+ }
+}
+
+task SummarizeDatasets {
+ input {
+ File databaseFile
+ String outputPrefix
+
+ File? datasetGroupsCSV
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ summarize_datasets \
+ ~{"--db " + databaseFile} \
+ ~{"--o " + outputPrefix} \
+ ~{"--groups " + datasetGroupsCSV}
+ }
+
+ output {
+ File outputSummaryFile = outputPrefix + "_talon_summary.tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ databaseFile: "TALON database."
+ outputPrefix: "Output directory path + output file prefix."
+ datasetGroupsCSV: "File of comma-delimited dataset groups to process together."
+
+ outputSummaryFile: "Tab-delimited file of gene and transcript counts for each dataset."
+ }
+}
+
+task Talon {
+ input {
+ File SAMfile
+ File configFile
+ File databaseFile
+ String outputPrefix
+ String genomeBuild
+ String configFileName = basename(configFile)
+ String SAMfileName = basename(SAMfile)
+ Float minimumCoverage = 0.9
+ Int minimumIdentity = 0
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/talon:v4.2_cv2"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ mv ${configFile} ./${configFileName}
+ mv ${SAMfile} ./${SAMfileName}
+ talon \
+ ~{"--f " + configFileName} \
+ ~{"--db " + databaseFile} \
+ ~{"--o " + outputPrefix} \
+ ~{"--build " + genomeBuild} \
+ ~{"--cov " + minimumCoverage} \
+ ~{"--identity " + minimumIdentity}
+ }
+
+ output {
+ File outputUpdatedDatabase = databaseFile
+ File outputLog = outputPrefix + "_talon_QC.log"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ SAMfile: "Input SAM file, same one as described in configFile."
+ configFile: "Dataset config file."
+ databaseFile: "TALON database. Created using initialize_talon_database.py."
+ outputPrefix: "Output directory path + output file prefix."
+ genomeBuild: "Genome build (i.e. hg38) to use."
+ minimumCoverage: "Minimum alignment coverage in order to use a SAM entry."
+ minimumIdentity: "Minimum alignment identity in order to use a SAM entry."
+
+ outputUpdatedDatabase: "Updated TALON database."
+ outputLog: "Log file from TALON run."
+ }
+}
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..7afd24197084d5ac318b07a15bc2692b38ece5f5
--- /dev/null
+++ b/transcriptclean.wdl
@@ -0,0 +1,253 @@
+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task CleanSpliceJunctions {
+ input {
+ File SAMfile
+ File referenceGenome
+ String outputPrefix
+ File spliceJunctionAnnotation
+
+ File? variantFile
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ clean_splice_jns \
+ ~{"--f=" + SAMfile} \
+ ~{"--g=" + referenceGenome} \
+ ~{"--o=" + outputPrefix} \
+ ~{"--s=" + spliceJunctionAnnotation} \
+ ~{"--v=" + variantFile}
+ }
+
+ output {
+ File outputCleanedSAM = outputPrefix + "_clean.sam"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ SAMfile: "Input SAM file"
+ referenceGenome: "Reference genome fasta file."
+ outputPrefix: "Output directory path + output file prefix."
+ spliceJunctionAnnotation: "Splice junction file"
+ variantFile: "VCF formatted file of variants"
+
+ outputCleanedSAM: "Cleaned sam output file."
+ }
+}
+
+task GetCorrectedSJsFromLog {
+ input {
+ File TElogFile
+ String outputPrefix
+
+ Int cores = 1
+ Int memory = 5
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ get_corrected_SJs_from_log \
+ ~{TElogFile} \
+ ~{outputPrefix + ".tsv"}
+ }
+
+ output {
+ File outputCorrectedSJs = outputPrefix + ".tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ TElogFile: "TE log from TranscriptClean."
+ outputPrefix: "Output directory path + output file prefix."
+
+ outputCorrectedSJs: "Formely noncanonical splice junctions in BED format."
+ }
+}
+
+task GetSJsFromGtf {
+ input {
+ File GTFfile
+ File genomeFile
+ String outputPrefix
+ Int minIntronSize = 21
+
+ Int cores = 1
+ Int memory = 8
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ get_SJs_from_gtf \
+ ~{"--f=" + GTFfile} \
+ ~{"--g=" + genomeFile} \
+ ~{"--o=" + outputPrefix + ".tsv"} \
+ ~{"--minIntronSize=" + minIntronSize}
+ }
+
+ output {
+ File outputSJsFile = outputPrefix + ".tsv"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ GTFfile: "Input GTF file"
+ genomeFile: "Reference genome"
+ outputPrefix: "Output directory path + output file prefix."
+ minIntronSize: "Minimum size of intron to consider a junction."
+
+ outputSJsFile: "Extracted splice junctions."
+ }
+}
+
+task GetTranscriptCleanStats {
+ input {
+ File transcriptCleanSAMfile
+ String outputPrefix
+
+ Int cores = 1
+ Int memory = 4
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ get_TranscriptClean_stats \
+ ~{transcriptCleanSAMfile} \
+ ~{outputPrefix}
+ }
+
+ output {
+ File outputStatsFile = stdout()
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ transcriptCleanSAMfile: "Output SAM file from TranscriptClean"
+ outputPrefix: "Output directory path + output file prefix."
+
+ outputStatsFile: "Summary stats from TranscriptClean run."
+ }
+}
+
+task TranscriptClean {
+ input {
+ File SAMfile
+ File referenceGenome
+ String outputPrefix
+ Int maxLenIndel = 5
+ Int maxSJoffset = 5
+ Boolean correctMismatches = true
+ Boolean correctIndels = true
+ Boolean dryRun = false
+ Boolean primaryOnly = false
+
+ File? spliceJunctionAnnotation
+ File? variantFile
+ Boolean? correctSJs
+
+ Int cores = 1
+ Int memory = 25
+ String dockerImage = "biocontainers/transcriptclean:v1.0.7_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{outputPrefix})
+ TranscriptClean \
+ ~{"-s " + SAMfile} \
+ ~{"-g " + referenceGenome} \
+ ~{"-o " + outputPrefix} \
+ ~{"-j " + spliceJunctionAnnotation} \
+ ~{"-v " + variantFile} \
+ ~{"--maxLenIndel=" + maxLenIndel} \
+ ~{"--maxSJOffset=" + maxSJoffset} \
+ ~{true="-m CORRECTMISMATCHES" false="-m false" correctMismatches} \
+ ~{true="-i CORRECTINDELS" false="-i false" correctIndels} \
+ ~{true="--correctSJs=CORRECTSJS" false="--correctSJs=false" correctSJs} \
+ ~{true="--dryRun" false="" dryRun} \
+ ~{true="--primaryOnly" false="" primaryOnly}
+ }
+
+ output {
+ File outputTranscriptCleanFasta = outputPrefix + "_clean.fa"
+ File outputTranscriptCleanLog = outputPrefix + "_clean.log"
+ File outputTranscriptCleanSAM = outputPrefix + "_clean.sam"
+ File outputTranscriptCleanTElog = outputPrefix + "_clean.TE.log"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ SAMfile: "Input SAM file containing transcripts to correct."
+ referenceGenome: "Reference genome fasta file."
+ outputPrefix: "Output directory path + output file prefix."
+ spliceJunctionAnnotation: "Splice junction file"
+ maxLenIndel: "Maximum size indel to correct."
+ maxSJoffset: "Maximum distance from annotated splice junction to correct."
+ correctMismatches: "Set this to make TranscriptClean correct mismatches."
+ correctIndels: "Set this to make TranscriptClean correct indels."
+ correctSJs: "Set this to make TranscriptClean correct splice junctions."
+ dryRun: "TranscriptClean will read in the data but don't do any correction."
+ primaryOnly: "TranscriptClean will only output primary mappings of transcripts."
+
+ outputTranscriptCleanFasta: "Fasta file containing corrected reads."
+ outputTranscriptCleanLog: "Log file of TranscriptClean run."
+ outputTranscriptCleanSAM: "SAM file containing corrected aligned reads."
+ outputTranscriptCleanTElog: "TE log file of TranscriptClean run."
+ }
+}
diff --git a/vardict.wdl b/vardict.wdl
index 0cbf38acd7a69f22e4b760f7f17932f585a52852..69a5441c22f47afccf011bddf98fb4888c10c989 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -20,6 +20,13 @@ task VarDict {
Int endColumn = 3
Int geneColumn = 4
+ Boolean outputCandidateSomaticOnly = true
+ Boolean outputAllVariantsAtSamePosition = true
+ Float mappingQuality = 20
+ Int minimumTotalDepth = 8
+ Int minimumVariantDepth = 4
+ Float minimumAlleleFrequency = 0.02
+
Int threads = 1
Int memory = 16
Float memoryMultiplier = 2.5
@@ -45,6 +52,12 @@ task VarDict {
~{true="var2vcf_paired.pl" false="var2vcf_valid.pl" defined(normalBam)} \
-N "~{tumorSampleName}~{"|" + normalSampleName}" \
~{true="" false="-E" defined(normalBam)} \
+ ~{true="-M" false="" outputCandidateSomaticOnly} \
+ ~{true="-A" false="" outputAllVariantsAtSamePosition} \
+ -Q ~{mappingQuality} \
+ -d ~{minimumTotalDepth} \
+ -v ~{minimumVariantDepth} \
+ -f ~{minimumAlleleFrequency} \
> ~{outputVcf}
}