fix some issues, add flagstat

bcftools.wdl

@@ -106,7 +106,6 @@ task Annotate {
         inputFile: {description: "A vcf or bcf file.", category: "required"}
         inputFileIndex: {description: "The index for the input vcf or bcf.", category: "common"}
         outputPath: {description: "The location the output VCF file should be written.", category: "common"}
-        outputType: {description: "Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf", category: "advanced"}
         annsFile: {description: "Bgzip-compressed and tabix-indexed file with annotations (see man page for details).", category: "common"}
         annsFileIndex: {description: "The index for annsFile.", category: "common"}
         collapse: {description: "Treat as identical records with <snps|indels|both|all|some|none>, see man page for details.", category: "advanced"}

hmftools.wdl

@@ -341,7 +341,7 @@ task Linx {
         String memory = "9G"
         String javaXmx = "8G"
         Int timeMinutes = 30
-        String dockerImage = "docker://quay.io/biocontainers/hmftools-linx:1.12--0"
+        String dockerImage = "quay.io/biocontainers/hmftools-linx:1.12--0"
     }
 
     command {
@@ -381,6 +381,10 @@ task Linx {
         File linxVisSegments = "~{outputDir}/~{sampleName}.linx.vis_segments.tsv"
         File linxVisSvData = "~{outputDir}/~{sampleName}.linx.vis_sv_data.tsv"
         File linxVersion = "~{outputDir}/linx.version"
+        Array[File] outputs = [driverCatalog, linxBreakend, linxClusters, linxDrivers, linxFusion,
+                               linxLinks, linxSvs, linxViralInserts, linxVisCopyNumber,
+                               linxVisFusion, linxVisGeneExon, linxVisProteinDomain,
+                               linxVisSegments, linxVisSvData, linxVersion]
     }
 
     runtime {

picard.wdl

@@ -473,10 +473,10 @@ task CollectWgsMetrics {
         CollectWgsMetrics \
         REFERENCE_SEQUENCE=~{referenceFasta} \
         INPUT=~{inputBam} \
-        OUTPUT=~{outputPath} \ 
+        OUTPUT=~{outputPath} \
         ~{"MINIMUM_MAPPING_QUALITY=" + minimumMappingQuality} \
         ~{"MINIMUM_BASE_QUALITY=" + minimumBaseQuality} \
-        ~{"OVERAGE_CAP=" + coverageCap}
+        ~{"COVERAGE_CAP=" + coverageCap}
     }
 
     output {

sambamba.wdl

@@ -20,6 +20,49 @@ version 1.0
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
+task Flagstat {
+    input {
+        File inputBam
+        File inputBamIndex
+        String outputPath = "./flagstat.txt"
+
+        Int threads = 2
+        String memory = "8G"
+        Int timeMinutes = 120
+        String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
+    }
+
+    command {
+        sambamba flagstat \
+	    -t ~{threads} \
+	    ~{inputBam} \
+        > ~{outputPath}
+    }
+
+    output {
+        File stats = outputPath
+    }
+
+    runtime {
+        cpu: threads
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        inputBam: {description: "The input BAM file.", category: "required"}
+        inputBamIndex: {description: "The index for the BAM file.", category: "required"}
+        outputPath: {description: "The path to write the ouput to.", category: "required"}
+
+        threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+        memory: {description: "The amount of memory available to the job.", 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"}
+    }
+}
+
+
 task Markdup {
     input {
         Array[File] inputBams