Merge pull request #292 from biowdl/famm-run

Famm run

CHANGELOG.md

@@ -9,6 +9,7 @@ that users understand how the changes affect the new version.
 -->
 version 5.0.1
 ---------------------------
++ Smoove: enable genotyping
 + add runtime memory to number of tasks.
 
 version 5.0.0

bcftools.wdl

@@ -43,7 +43,7 @@ task Annotate {
         File? regionsFile
         File? renameChrs
         File? samplesFile
-        
+
         Int threads = 0
         String memory = "256M"
         Int timeMinutes = 1 + ceil(size(inputFile, "G"))
@@ -53,7 +53,7 @@ task Annotate {
     Boolean compressed = basename(outputPath) != basename(outputPath, ".gz")
 
     command {
-        set -e 
+        set -e
         mkdir -p "$(dirname ~{outputPath})"
         bcftools annotate \
         -o ~{outputPath} \
@@ -154,7 +154,7 @@ task Sort {
         File outputVcf = outputPath
         File? outputVcfIndex = outputPath + ".tbi"
     }
-    
+
     runtime {
         memory: memory
         time_minutes: timeMinutes

smoove.wdl

@@ -41,11 +41,13 @@ task Call {
         --outdir ~{outputDir} \
         --name ~{sample} \
         --fasta ~{referenceFasta} \
+        --removepr \
+        --genotype \
         ~{bamFile}
     }
 
     output {
-        File smooveVcf = outputDir + "/" + sample + "-smoove.vcf.gz"
+        File smooveVcf = outputDir + "/" + sample + "-smoove.genotyped.vcf.gz"
     }
 
     runtime {