From 4c8beab83261e57e7b68744613f0192915e1d716 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 22 Aug 2024 11:35:06 +0200
Subject: [PATCH] minor changes

---
 src/fastqc/config.vsh.yaml | 6 +++---
 src/fastqc/test.sh         | 6 +++++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/fastqc/config.vsh.yaml b/src/fastqc/config.vsh.yaml
index 942e7c18..724f5c2d 100644
--- a/src/fastqc/config.vsh.yaml
+++ b/src/fastqc/config.vsh.yaml
@@ -25,7 +25,7 @@ argument_groups:
         
   - name: Outputs
     description: |
-      At least one of the output options (--html or --zip) must be used:
+      At least one of the output options (--html or --zip) must be used.
     arguments:
 
       - name: --html
@@ -39,7 +39,7 @@ argument_groups:
           e.g. 
             --input "sample_1.fq"
             --html "*.html"
-            would create a html file named sample_1.html
+            would create an output html file named sample_1.html
         example: "*.html"
       
       - name: --zip
@@ -53,7 +53,7 @@ argument_groups:
           e.g. 
             --input "sample_1.fq"
             --html "*.zip"
-            would create a zip file named sample_1.zip
+            would create an output zip file named sample_1.zip
         example: "*.zip"    
 
   - name: Options
diff --git a/src/fastqc/test.sh b/src/fastqc/test.sh
index 8f8af212..543e3458 100644
--- a/src/fastqc/test.sh
+++ b/src/fastqc/test.sh
@@ -109,6 +109,7 @@ echo "-> Run Test1: one input"
   --input "../input_1.fq" \
   --html "*_fastqc.html" \
   --zip "*_fastqc.zip" \
+  --quiet \
 
 assert_file_exists "input_1_fastqc.html"
 assert_file_exists "input_1_fastqc.zip"
@@ -133,6 +134,7 @@ echo "-> Run Test2: two inputs"
   --input "../input_2.fq" \
   --html "*_fastqc.html" \
   --zip "*_fastqc.zip" \
+  --quiet \
 
 # File 1
 assert_file_exists "input_1_fastqc.html"
@@ -165,7 +167,7 @@ echo "-> Run Test3: contaminants"
   --contaminants "../contaminants.txt" \
   --html "*_fastqc.html" \
   --zip "*_fastqc.zip" \
-
+  --quiet \
 
 assert_file_exists "input_1_fastqc.html"
 assert_file_exists "input_1_fastqc.zip"
@@ -190,6 +192,7 @@ echo "-> Run Test4: sam file"
   --format "sam" \
   --html "*_fastqc.html" \
   --zip "*_fastqc.zip" \
+  --quiet \
 
 assert_file_exists "example_fastqc.html"
 assert_file_exists "example_fastqc.zip"
@@ -218,6 +221,7 @@ echo "-> Run Test5: multiple options"
   --kmers 5 \
   --html "*_fastqc.html" \
   --zip "*_fastqc.zip" \
+  --quiet \
 # --casava \
 
 assert_file_exists "input_1_fastqc.html"