Merge pull request #40 from biowdl/various_new_tasks

Add Various new tasks

README.md

+# Tasks
+
+This repository contains the WDL task definitions used in the various 
+[Biowdl](https://github.com/biowdl) workflows and pipelines.
+
+
+## Documentation
+
+Documentation for this workflow can be found 
+[here](https://biowdl.github.io/tasks/).
+
+## About
+These tasks are part of [Biowdl](https://github.com/biowdl)
+developed by [the SASC team](http://sasc.lumc.nl/). 
+
+## Contact
+
+<p>
+  <!-- Obscure e-mail address for spammers -->
+For any question related to these tasks, please use the
+<a href='https://github.com/biowdl/tasks/issues'>github issue tracker</a>
+or contact
+ <a href='http://sasc.lumc.nl/'>the SASC team</a> directly at: <a href='&#109;&#97;&#105;&#108;&#116;&#111;&#58;&#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;'>
+&#115;&#97;&#115;&#99;&#64;&#108;&#117;&#109;&#99;&#46;&#110;&#108;</a>.
+</p>

biopet.wdl

@@ -417,3 +417,71 @@ task ValidateVcf {
         memory: ceil(memory * memoryMultiplier)
     }
 }
+
+task VcfStats {
+    input {
+        File vcfFile
+        File vcfIndex
+        File refFasta
+        File refFastaIndex
+        File refDict
+        String outDir
+        File? intervals
+        Array[String]+? infoTags
+        Array[String]+? genotypeTags
+        Int? sampleToSampleMinDepth
+        Int? binSize
+        Int? maxContigsInSingleJob
+        Boolean writeBinStats = false
+        Int localThreads = 1
+        Boolean notWriteContigStats = false
+        Boolean skipGeneral = false
+        Boolean skipGenotype = false
+        Boolean skipSampleDistributions = false
+        Boolean skipSampleCompare = false
+        String? sparkMaster
+        Int? sparkExecutorMemory
+        Array[String]+? sparkConfigValues
+
+        Int memory = 4
+        Float memoryMultiplier = 2.0
+        File? toolJar
+        String? preCommand
+    }
+
+    String toolCommand = if defined(toolJar)
+        then "java -Xmx" + memory + "G -jar " + toolJar
+        else "biopet-vcfstats -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        -I ~{vcfFile} \
+        -R ~{refFasta} \
+        -o ~{outDir} \
+        -t ~{localThreads} \
+        ~{"--intervals " + intervals} \
+        ~{true="--infoTag" false="" defined(infoTags)} ~{sep=" --infoTag " infoTags} \
+        ~{true="--genotypeTag" false="" defined(genotypeTags)} ~{sep=" --genotypeTag "
+            genotypeTags} \
+        ~{"--sampleToSampleMinDepth " + sampleToSampleMinDepth} \
+        ~{"--binSize " + binSize} \
+        ~{"--maxContigsInSingleJob " + maxContigsInSingleJob} \
+        ~{true="--writeBinStats" false="" writeBinStats} \
+        ~{true="--notWriteContigStats" false="" notWriteContigStats} \
+        ~{true="--skipGeneral" false="" skipGeneral} \
+        ~{true="--skipGenotype" false="" skipGenotype} \
+        ~{true="--skipSampleDistributions" false="" skipSampleDistributions} \
+        ~{true="--skipSampleCompare" false="" skipSampleCompare} \
+        ~{"--sparkMaster " + sparkMaster} \
+        ~{"--sparkExecutorMemory " + sparkExecutorMemory} \
+        ~{true="--sparkConfigValue" false="" defined(sparkConfigValues)} ~{
+            sep=" --sparkConfigValue" sparkConfigValues}
+    }
+
+    runtime {
+        cpu: localThreads
+        memory: ceil(memory * memoryMultiplier)
+    }
+}

gatk.wdl

@@ -293,6 +293,51 @@ task HaplotypeCallerGvcf {
     }
 }
 
+task MuTect2 {
+    input {
+        String? preCommand
+
+        Array[File]+ inputBams
+        File inputBamIndex
+        File refFasta
+        File refFastaIndex
+        File refDict
+        String outputVcf
+        String tumorSample
+        String? normalSample
+        Array[File]+ intervals
+
+        String? gatkJar
+        Int memory = 4
+        Float memoryMultiplier = 3
+    }
+
+    String toolCommand = if defined(gatkJar)
+        then "java -Xmx" + memory + "G -jar " + gatkJar
+        else "gatk --java-options -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        Mutect2 \
+        -R ~{refFasta} \
+        -I ~{sep=" -I " inputBams} \
+        -tumor ~{tumorSample} \
+        ~{"-normal " + normalSample} \
+        -O ~{outputVcf} \
+        -L ~{sep=" -L " intervals}
+    }
+
+    output {
+        File vcfFile = outputVcf
+    }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
+}
+
 task SplitNCigarReads {
     input {
         String? preCommand

strelka.wdl

+version 1.0
+
+task Somatic {
+    input {
+        String? preCommand
+        String? installDir
+        String runDir
+        File normalBam
+        File tumorBam
+        File refFasta
+
+        Int cores = 1
+        Int memory = 4
+    }
+
+    String toolCommand = if defined(installDir)
+        then installDir + "bin/configureStrelkaSomaticWorkflow.py"
+        else "configureStrelkaSomaticWorkflow.py"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        --normalBam ~{normalBam} \
+        --tumorBam ~{tumorBam} \
+        --ref ~{refFasta} \
+        --runDir ~{runDir}
+
+        ~{runDir}/runWorkflow.py \
+        -m local \
+        -J ~{cores} \
+        -g ~{memory}
+    }
+
+    output {
+        File indelsVcf = runDir + "/results/variants/somatic.indels.vcf.gz"
+        File indelsIndex = runDir + "/results/variants/somatic.indels.vcf.gz.tbi"
+        File snvVcf = runDir + "/results/variants/somatic.snvs.vcf.gz"
+        File snvIndex = runDir + "/results/variants/somatic.snvs.vcf.gz.tbi"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+    }
+}
\ No newline at end of file

vardict.wdl

+version 1.0
+
+task VarDict {
+    input {
+        String? installDir
+
+        File tumorBam
+        File normalBam
+        File refFasta
+        File bedFile
+        String tumorSampleName
+        String normalSampleName
+        String outputVcf
+
+        Int chromosomeColumn = 1
+        Int startColumn = 2
+        Int endColumn = 3
+        Int geneColumn = 4
+
+        String? preCommand
+    }
+
+    String toolCommand = if defined(installDir)
+        then installDir + "/VarDict"
+        else "vardict"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        -G ~{refFasta} \
+        -N ~{tumorSampleName} \
+        -b "~{tumorBam}|~{normalBam}" \
+        -c ~{chromosomeColumn} \
+        -S ~{startColumn} \
+        -E ~{endColumn} \
+        -g ~{geneColumn} \
+        ~{bedFile} | \
+        ~{installDir + "/"}testsomatic.R | \
+        ~{installDir + "/"}var2vcf_paired.pl \
+        -N "~{tumorSampleName}|~{normalSampleName}" \
+        > ~{outputVcf}
+    }
+
+    output {
+        File vcfFile = outputVcf
+    }
+}
\ No newline at end of file