From 76e9624e3f04e573a56c1443884b2ca385488319 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 30 Mar 2022 11:31:37 +0200
Subject: [PATCH] NOW commit the adapte rtrim flag

---
 conf/modules.config  | 2 +-
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index a9bc3a1..71eaa75 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -68,7 +68,7 @@ process {
             // collapsing options - option to retain singletons
             params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
             // trimming options
-            params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
+            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
             params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
             !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
             // filtering options
diff --git a/nextflow.config b/nextflow.config
index a312d0c..6fde513 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,7 +57,7 @@ params {
     // FASTQ preprocessing
     shortread_clipmerge                     = false
     shortread_clipmerge_tool                = 'fastp'
-    shortread_clipmerge_skiptrim            = false
+    shortread_clipmerge_skipadaptertrim     = false
     shortread_clipmerge_mergepairs          = false
     shortread_clipmerge_excludeunmerged     = true
     shortread_clipmerge_adapter1            = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 545f990..adc5a73 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -286,7 +286,7 @@
             "type": "string",
             "default": "fastp"
         },
-        "shortread_clipmerge_skiptrim": {
+        "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
         },
         "shortread_clipmerge_mergepairs": {