Merge branch 'develop' into BIOWDL-6

biopet.wdl

@@ -244,6 +244,39 @@ task SampleConfig {
     }
 }
 
+task SampleConfigCromwellArrays {
+    input {
+        File? toolJar
+        String? preCommand
+        Array[File]+ inputFiles
+        String outputPath
+
+        Int memory = 4
+        Float memoryMultiplier = 2.0
+    }
+
+    String toolCommand = if defined(toolJar)
+        then "java -Xmx" + memory + "G -jar " + toolJar
+        else "biopet-sampleconfig -Xmx" + memory + "G"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        mkdir -p $(dirname ~{outputPath})
+        ~{toolCommand} CromwellArrays \
+        -i ~{sep="-i " inputFiles} \
+        ~{"-o " + outputPath}
+    }
+
+    output {
+        File outputFile = outputPath
+    }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
+}
+
 task ScatterRegions {
     input {
         String? preCommand
@@ -425,7 +458,7 @@ task VcfStats {
         File refFasta
         File refFastaIndex
         File refDict
-        String outDir
+        String outputDir
         File? intervals
         Array[String]+? infoTags
         Array[String]+? genotypeTags
@@ -455,11 +488,12 @@ task VcfStats {
 
     command {
         set -e -o pipefail
+        mkdir -p ~{outputDir}
         ~{preCommand}
         ~{toolCommand} \
         -I ~{vcfFile} \
         -R ~{refFasta} \
-        -o ~{outDir} \
+        -o ~{outputDir} \
         -t ~{localThreads} \
         ~{"--intervals " + intervals} \
         ~{true="--infoTag" false="" defined(infoTags)} ~{sep=" --infoTag " infoTags} \
@@ -480,6 +514,58 @@ task VcfStats {
             sep=" --sparkConfigValue" sparkConfigValues}
     }
 
+    output {
+        File? general = outputDir + "/general.tsv"
+        File? genotype = outputDir + "/genotype.tsv"
+        File? sampleDistributionAvailableAggregate = outputDir +
+            "/sample_distributions/Available.aggregate.tsv"
+        File? sampleDistributionAvailable = outputDir + "/sample_distributions/Available.tsv"
+        File? sampleDistributionCalledAggregate = outputDir +
+            "/sample_distributions/Called.aggregate.tsv"
+        File? sampleDistributionCalled = outputDir + "/sample_distributions/Called.tsv"
+        File? sampleDistributionFilteredAggregate = outputDir +
+            "/sample_distributions/Filtered.aggregate.tsv"
+        File? sampleDistributionFiltered = outputDir + "/sample_distributions/Filtered.tsv"
+        File? sampleDistributionHetAggregate = outputDir + "/sample_distributions/Het.aggregate.tsv"
+        File? sampleDistributionHetNoNRefAggregate = outputDir +
+            "/sample_distributions/HetNonRef.aggregate.tsv"
+        File? sampleDistributionHetNonRef = outputDir + "/sample_distributions/HetNonRef.tsv"
+        File? sampleDistributionHet = outputDir + "/sample_distributions/Het.tsv"
+        File? sampleDistributionHomAggregate = outputDir + "/sample_distributions/Hom.aggregate.tsv"
+        File? sampleDistributionHomRefAggregate = outputDir +
+            "/sample_distributions/HomRef.aggregate.tsv"
+        File? sampleDistributionHomRef = outputDir + "/sample_distributions/HomRef.tsv"
+        File? sampleDistributionHom = outputDir + "/sample_distributions/Hom.tsv"
+        File? sampleDistributionHomVarAggregate = outputDir +
+            "/sample_distributions/HomVar.aggregate.tsv"
+        File? sampleDistributionHomVar = outputDir + "/sample_distributions/HomVar.tsv"
+        File? sampleDistributionMixedAggregate = outputDir +
+            "/sample_distributions/Mixed.aggregate.tsv"
+        File? sampleDistributionMixed = outputDir + "/sample_distributions/Mixed.tsv"
+        File? sampleDistributionNoCallAggregate = outputDir +
+            "/sample_distributions/NoCall.aggregate.tsv"
+        File? sampleDistributionNoCall = outputDir + "/sample_distributions/NoCall.tsv"
+        File? sampleDistributionNonInformativeAggregate = outputDir +
+            "/sample_distributions/NonInformative.aggregate.tsv"
+        File? sampleDistributionNonInformative = outputDir +
+            "/sample_distributions/NonInformative.tsv"
+        File? sampleDistributionToalAggregate = outputDir +
+            "/sample_distributions/Total.aggregate.tsv"
+        File? sampleDistributionTotal = outputDir + "/sample_distributions/Total.tsv"
+        File? sampleDistributionVariantAggregate = outputDir +
+            "/sample_distributions/Variant.aggregate.tsv"
+        File? sampleDistributionVariant = outputDir + "/sample_distributions/Variant.tsv"
+        File? sampleCompareAlleleAbs = outputDir + "/sample_compare/allele.abs.tsv"
+        File? sampleCompareAlleleNonRefAbs = outputDir + "/sample_compare/allele.non_ref.abs.tsv"
+        File? sampleCompareAlleleRefAbs = outputDir + "/sample_compare/allele.ref.abs.tsv"
+        File? sampleCompareAlleleRel = outputDir + "/sample_compare/allele.rel.tsv"
+        File? sampleCompareGenotypeAbs = outputDir + "/sample_compare/genotype.abs.tsv"
+        File? sampleCompareGenotypeNonRefAbs = outputDir +
+            "/sample_compare/genotype.non_ref.abs.tsv"
+        File? sampleCompareGenotypeRefAbs = outputDir + "/sample_compare/genotype.ref.abs.tsv"
+        File? sampleCompareGenotypeRel = outputDir + "/sample_compare/genotype.rel.tsv"
+    }
+
     runtime {
         cpu: localThreads
         memory: ceil(memory * memoryMultiplier)

bwa.wdl

@@ -5,8 +5,7 @@ task Mem {
         String? preCommand
         File inputR1
         File? inputR2
-        File referenceFasta
-        Array[File] indexFiles # These indexFiles need to be added, otherwise cromwell will not find them.
+        BwaIndex bwaIndex
         String outputPath
         String? readgroup
 
@@ -20,7 +19,7 @@ task Mem {
         ~{preCommand}
         bwa mem ~{"-t " + threads} \
         ~{"-R '" + readgroup + "'"} \
-        ~{referenceFasta} \
+        ~{bwaIndex.fastaFile} \
         ~{inputR1} \
         ~{inputR2} \
         | samtools sort --output-fmt BAM - > ~{outputPath}
@@ -75,3 +74,7 @@ task Index {
     }
 }
 
+struct BwaIndex {
+    File fastaFile
+    Array[File] indexFiles
+}

common.wdl

@@ -134,3 +134,9 @@ task StringArrayMd5 {
         memory: 1
     }
 }
+
+struct Reference {
+    File fasta
+    File fai
+    File dict
+}