remove outputPathBamIndex as input

samtools.wdl

@@ -400,9 +400,10 @@ task FilterShortReadsBam {
     input {
         File bamFile
         String outputPathBam
-        String outputPathBamIndex
         String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
     }
+    
+    String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
 
     command {
         set -e
@@ -425,7 +426,6 @@ task FilterShortReadsBam {
     parameter_meta {
         bamFile: {description: "The bam file to process.", category: "required"}
         outputPathBam: {description: "The filtered bam file.", category: "required"}
-        outputPathBamIndex: {description: "The index of filtered bam file.", category: "required"}
         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"}
     }
 }