From d3d28da1b18d60fa406e9c175f25d49396245084 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 2 Jun 2022 11:53:53 +0200
Subject: [PATCH] Update after review

---
 conf/modules.config  | 4 ++--
 conf/test.config     | 4 ++--
 nextflow.config      | 4 ++--
 nextflow_schema.json | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 164fe91..09b2ed9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -137,8 +137,8 @@ process {
     withName: FILTLONG {
         ext.args = [
             "--min_length ${params.longread_qc_minlength}",
-            "--keep_percent ${params.longread_qc_keepbppercent}",
-            "--target_bases ${params.longread_qc_targetnbases}"
+            "--keep_percent ${params.longread_qc_keep_percent}",
+            "--target_bases ${params.longread_qc_target_bases}"
         ]
         .join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
diff --git a/conf/test.config b/conf/test.config
index 6af771c..d6fc7fe 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,8 +24,8 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
     databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
-    perform_shortread_qc           = true
-    perform_longread_qc                 = false
+    perform_shortread_qc                  = true
+    perform_longread_qc                   = true
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true
diff --git a/nextflow.config b/nextflow.config
index 5e9b385..d8f80ab 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -68,8 +68,8 @@ params {
     longread_qc_run_clip             = false
     longread_qc_run_filter           = false
     longread_qc_minlength            = 1000
-    longread_qc_keepbppercent        = 90
-    longread_qc_targetnbases         = 500000000
+    longread_qc_keep_percent        = 90
+    longread_qc_target_bases         = 500000000
 
     save_preprocessed_reads          = false
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c38e5d1..e3cc558 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -420,11 +420,11 @@
             "type": "integer",
             "default": 1000
         },
-        "longread_qc_keepbppercent": {
+        "longread_qc_keep_percent": {
             "type": "integer",
             "default": 90
         },
-        "longread_qc_targetnbases": {
+        "longread_qc_target_bases": {
             "type": "integer",
             "default": 500000000
         }