From a97bb69cd28d93b4bae24b99014a6e5e6148c548 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 23 Aug 2022 14:24:57 +0200
Subject: [PATCH] Prettier

---
 assets/multiqc_config.yml | 1 +
 conf/modules.config       | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 8df4c5e..d16ed7e 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -21,6 +21,7 @@ run_modules:
   - bowtie2
   - kraken
   - malt
+  - custom_content
 
 #extra_fn_clean_exts:
 #    - '_fastp'
diff --git a/conf/modules.config b/conf/modules.config
index 0330abb..1f4914d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -241,7 +241,8 @@ process {
     withName: PRINSEQPLUSPLUS {
         ext.args =  [
                 params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
-                "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0"
+                "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
+                "-VERBOSE 2"
             ].join(' ').trim()
         ext.prefix = { "${meta.id}-${meta.run_accession}" }
         publishDir = [