add publishDir on bam filtering subworkflow in Nextflow

structuralvariants/nextflow/modules/samtools_index.nf

+params.bamsDir = ""
+
 process SAMTOOLS_INDEX {
   tag { "samtools index" }
   container 'quay.io/biocontainers/samtools:1.5--2'
 
+  publishDir "${params.outputDir}/${params.bamsDir}", enabled: params.bamsDir, mode: 'copy'
+
   input:
     path input
 

structuralvariants/nextflow/subworkflows/bam_filtering.nf

+params.bamsDir = "output_bams"
+
 /*
  * Include for bam_filtering
 */
@@ -6,7 +8,7 @@ include {
 } from "../modules/samtools_view"
 include {
     SAMTOOLS_INDEX
-} from "../modules/samtools_index"
+} from "../modules/samtools_index" params([*:params, "bamsDir": ""])
 
 
 /*