adjusted paramet names and help text, per review

Author: ilight1542

conf/test_microbial.config

@@ -44,7 +44,7 @@ params {
 
     // BAM filtering
     deduplication_tool                    = "dedup"
-    deduplication_mergejobs               = true
+    deduplication_skipregionsplit               = true
     run_bamfiltering                      = true
     bamfiltering_minreadlength            = 30
     bamfiltering_mappingquality           = 37

nextflow.config

@@ -199,7 +199,7 @@ params {
 
     // Deduplication options
     skip_deduplication                                               = false
-    deduplication_mergejobs                                          = false
+    deduplication_skipregionsplit                                    = false
     deduplication_tool                                               = 'markduplicates'
 
     // Qualimap

nextflow_schema.json

@@ -1002,10 +1002,11 @@
                     "description": "Specify to skip the removal of PCR duplicates.",
                     "fa_icon": "fas fa-forward"
                 },
-                "deduplication_mergejobs": {
+                "deduplication_skipregionsplit": {
                     "type": "boolean",
                     "description": "Specify to run deduplicaiton without splitting bams by contig (default behavior).",
-                    "fa_icon": "fas fa-forward"
+                    "fa_icon": "fas fa-forward",
+                    "help_text":  "Run deduplication steps bam-by-bam rather than contig-by-contig for each bam file. This reduces the total number of jobs submitted to a cluster, but increases the computational runtime. If you use a shared cluster with limited resources, running many low-resource jobs can slow down the overall runtime of eager due to scheduling constraints.\nAlso applicable for poor-quality reference genomes." 
                 },
                 "deduplication_tool": {
                     "type": "string",

subworkflows/local/deduplicate.nf

@@ -29,7 +29,7 @@ workflow DEDUPLICATE {
         addNewMetaFromAttributes( it, "id" , "reference" , false )
     }
 
-    if ( params.deduplication_mergejobs ) {
+    if ( params.deduplication_skipregionsplit ) {
 
         // No splitting of .bam files by contig, deduplicate all in one
         input_for_deduplication = ch_bam_bai
@@ -110,7 +110,7 @@ workflow DEDUPLICATE {
         ch_dedupped_bam = DEDUP.out.bam
     }
 
-    if ( params.deduplication_mergejobs ) {
+    if ( params.deduplication_skipregionsplit ) {
 
         // Bams were never split by region, so bypass of re-merging
         ch_input_for_samtools_sort_dedupped = ch_dedupped_bam