From 03f7f7424d7660fafcb4608d42f9b58941105bd3 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 22 Aug 2024 11:12:19 +0200
Subject: [PATCH] tmpdir bug

---
 src/fastqc/config.vsh.yaml | 3 +--
 src/fastqc/script.sh       | 9 +++++----
 src/fastqc/test.sh         | 2 ++
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/fastqc/config.vsh.yaml b/src/fastqc/config.vsh.yaml
index bbc97a6c..942e7c18 100644
--- a/src/fastqc/config.vsh.yaml
+++ b/src/fastqc/config.vsh.yaml
@@ -25,8 +25,7 @@ argument_groups:
         
   - name: Outputs
     description: |
-      At least one of the following output options must be used:
-        --html, --zip
+      At least one of the output options (--html or --zip) must be used:
     arguments:
 
       - name: --html
diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh
index 9a3ab5e8..0eb1dad1 100644
--- a/src/fastqc/script.sh
+++ b/src/fastqc/script.sh
@@ -63,18 +63,19 @@ for file in "${input[@]}"; do
   # Removes everthing after the first dot of the basename
   sample_name=$(basename "${file}" | sed 's/\..*$//')
   if [[ -n "$par_html" ]]; then
-    input_html="$tempdir/${sample_name}_fastqc.html"
+    input_html="${tmpdir}/${sample_name}_fastqc.html"
     html_file="${par_html//\*/$sample_name}"
     mv "$input_html" "$html_file"
   fi
   if [[ -n "$par_zip" ]]; then
-    input_zip="$tempdir/${sample_name}_fastqc.zip"
+    input_zip="${tmpdir}/${sample_name}_fastqc.zip"
     zip_file="${par_zip//\*/$sample_name}"
     mv "$input_zip" "$zip_file"
   fi
   if [[ -n "$par_extract" ]]; then
-    # moves the extracted directory to the same directory as the input file
-    extract_dir="$tempdir/${sample_name}_fastqc"
+    # Moves the extracted directory to the same directory as the input file
+    extract_dir="${tmpdir}/${sample_name}_fastqc"
     mv "$extract_dir" "$file_dir"
   fi
 done
+
diff --git a/src/fastqc/test.sh b/src/fastqc/test.sh
index d12eb797..cfa8f7da 100644
--- a/src/fastqc/test.sh
+++ b/src/fastqc/test.sh
@@ -107,6 +107,8 @@ echo "-> Run Test1: one input"
 "$meta_executable" \
     --extract \
     --input "../input_1.fq" \
+    --html "*_fastqc.html" \
+    --zip "*_fastqc.zip" \
 
 assert_file_exists "input_1_fastqc.html"
 assert_file_exists "input_1_fastqc.zip"